Methods for identifying nucleic acid sequences

ABSTRACT

Embodiments relate to the detection of RNA in a sample of cells. More particularly, methods concern the localized detection of RNA in situ. The method relies on the conversion of RNA to complementary DNA prior to the targeting of the cDNA with a padlock probe(s). The hybridization of the padlock probe(s) relies on the nucleotide sequence of the cDNA which is derived from the corresponding nucleotide sequence of the target RNA. Rolling circle amplification of the subsequently circularized padlock probe produces a rolling circle product which may be detected. Advantageously, this allows the RNA to be detected in situ. In additional methods, rolling circle amplification products are sequenced.

This application claims priority to U.S. Provisional Application Ser. No. 61/692,090 filed Aug. 22, 2012; this application is also a continuation-in-part of U.S. patent application Ser. No. 13/397,503, filed Feb. 15, 2012, and PCT/US2012/25279 filed Feb. 15, 2012 both of which claim priority to U.S. Provisional Application Ser. No. 61/473,662, filed Apr. 8, 2011, and U.S. Provisional Application Ser. No. 61/442,921, filed Feb. 15, 2011; all of the above mentioned applications are hereby incorporated by reference in their entirety.

BACKGROUND

It is generally desirable to be able sensitively, specifically, qualitatively and/or quantitatively to detect RNA, and in particular mRNA, in a sample, including for example in fixed or fresh cells or tissues. It may be particularly desirable to detect an mRNA in a single cell. For example, in population-based assays that analyze the content of many cells, molecules in rare cells may escape detection. Furthermore, such assays provide no information concerning which of the molecules detected originate from which cells. Expression in single cells can vary substantially from the mean expression detected in a heterogeneous cell population. It is also desirable that single-cell studies may be performed with single-molecule sensitivity which allows the fluctuation and sequence variation in expressed transcripts to be studied. Fluorescence in situ hybridization (FISH) has previously been used to detect single mRNA molecules in situ. Although permitting determination of transcript copy numbers in individual cells, this technique cannot resolve highly similar sequences, so it cannot be used to study, for example, allelic inactivation or splice variation and cannot distinguish among gene family members.

The only option available for assigning transcript variants to a single cell in a given tissue involves polymerase chain reaction (PCR) of laser-capture microdissected material, which is time consuming and error prone, and thus not suitable for diagnostics.

As an alternative to PCR- and hybridization-based methods, padlock probes (Nilsson et al., 1994) have for many years been used to analyze nucleic acids. These highly selective probes are converted into circular molecules by target-dependent ligation upon hybridization to the target sequence. Circularized padlock probes can be amplified the localization of target molecules, including, where DNA targets are concerned, at the single-cell level. Such a protocol is described in Larrson et al., 2004), in which the target DNA molecule is used to prime the RCA reaction, causing the RCP to be anchored to the target molecule, thereby preserving its localization and improving the in situ detection.

While RNA molecules can also serve as templates for the ligation of padlock probes (Nilsson et al., 2000), RNA detection with padlock probes in situ has so far proven more difficult than DNA detection and is subject to limitations (Lagunavicius et al., 2009). For example, the high selectivity reported for padlock probes with in situ DNA detection and genotyping has not been reproduced with detection of RNA targets in situ. This is possibly due to problems with ligation of DNA molecules on an RNA template, since it is known that both the efficiency and the specificity of the ligation reaction are lower compared to ligation on a DNA template (Nilsson et al., 2000; Nilsson et al. 2001). It has recently been demonstrated that RNA molecules may be detected in situ with padlock probes and target-primed RCA (Lagunavicius et al., 2009; Stougaard et al., 2007). However, thus far, detection through target-primed RCA has for the most part been restricted to sequences in the 3′-end of non-polyadenylated RNA or sequences adjacent to the poly(A)-tail of mRNA. Since target-priming of the RCA reaction is dependent on a nearby free 3′-end that can be converted into an RCA primer, it is thought that this limitation results from the formation of RNA secondary structures which impede the polymerase action (3′ exonucleolysis) required to convert the RNA into a reaction primer. The detection efficiency of direct mRNA detection with padlock probes has been estimated to be as low as 1% (Nilsson et al., 2001). For the detection of non-polyadenylated RNA molecules, it has been noted that ligation of the probes using an internal hairpin structure as template resulted in higher detection efficiency than using the RNA molecule itself as ligation template (Stougaard et al., 2007). This indicates that better ligation conditions are required to be able to efficiently detect and genotype RNA directly with padlock probes in situ.

None of the methods for in situ detection of RNA presented thus far provide the possibility to detect sequence variation at the single nucleotide level and in particular to genotype transcripts. In the present embodiment, by converting an RNA target molecule into cDNA, the reduction in padlock probe ligation efficiency and specificity is avoided and the excellent genotyping properties provided by padlock probes are preserved. In addition, it has been found that unlike many previously described methods, embodiments are not restricted to detection of sequences positioned at specific sites in the RNA molecules.

SUMMARY OF THE INVENTION

Embodiments generally concern the characterization, detection, and/or identification of nucleic acid sequences using sensitive and specific padlock probes that are capable of distinguishing between sequences with as few as one nucleotide difference.

Some embodiments concern the detection of RNA, especially mRNA, in a sample of cells. More particularly, in particular embodiments methods concern the localized detection of RNA, particularly mRNA, in situ. In certain aspects, the method relies on the conversion of RNA to complementary DNA (cDNA) prior to the targeting of the cDNA with a padlock probe(s). The hybridization of the padlock probe(s) relies on the nucleotide sequence of the cDNA which is derived from the corresponding nucleotide sequence of the target RNA. Rolling circle amplification (RCA) of the subsequently circularized padlock probe produces a rolling circle product (RCP) which allows detection of the RNA. Advantageously, the RCP may be localized to the RNA allowing the RNA to be detected in situ. Also, provided are kits for performing such methods.

Methods and compositions advantageously allow for detection of RNA, and particularly, the detection of single nucleotide variations in RNA. For example, a detection resolution may be achieved that allows the study of differences in the relative expression of two allelic transcripts directly in tissue. Such studies have recently been recognized as important in the context of large-scale analyses of allele-specific expression, since it has been shown that many genes undergo this type of transcriptional regulation and that the allelic expression can differ among tissues. Furthermore, it has been shown that most human genes undergo alternative splicing, which could now be studied at the single-cell level using the methods described herein. No other in situ method exists today that can perform multiplex detection of expressed single nucleotide sequence variants in RNA. It is believed that the present method can meet this need, and that the ability it provides to visualize transcriptional variation directly in cells and tissues will be of value in both research and diagnostics, providing new insights about the human transcriptome.

Other methods and compositions can be used for one or more of the following: characterizing a target RNA, determining the sequence of a target RNA, determining the sequence of a target RNA by sequencing a complement of the target RNA, detecting in situ a target RNA, determining the sequence of a target RNA in situ, identifying sequence information for a target RNA, detecting in situ a nucleic acid and determining the sequence of the nucleic acid, identifying a cancer mutation in a target RNA, localizing a cancer mutation in a sample, identifying a cell expressing a mutant RNA, identifying a cell expressing an RNA associated with cancer, or analyzing a target RNA.

According to some methods, transcript detection in situ is accomplished by first converting the at least one mRNA into localized cDNA molecules that are detected with padlock probes and target-primed RCA (FIG. 1). Whilst of particular applicability to mRNA, the method may be used for the detection of any RNA molecule present in a cell, including but not limited to viral RNA, tRNA, rRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), microRNA (miRNA), small interfering RNA (siRNA), piwi-interacting RNA (piRNA), antisense RNA and non-coding RNA. The RNA is converted into cDNA, typically in a reverse transcriptase reaction comprising a reverse transcriptase enzyme and one or more reverse transcriptase primers. A ribonuclease is employed to digest the RNA in the resultant RNA:DNA duplex thus making the cDNA strand available for hybridization to a padlock probe(s). Hybridization of the padlock probe(s) to the cDNA allows circularization of the probe by direct or indirect ligation of the ends of the probe(s). The circularized padlock probe is then subjected to RCA and a RCP is detected by any appropriate means available in the art. The method may, in specific embodiments, also be used for localizing more than one target RNA, e.g., 2, 3, 4, 5, 6 or more target RNAs. These target RNAs may be derived from the same gene, or from different genes, or be derived from the same genomic sequence, or from different genomic sequences.

In one embodiment, there are methods for in situ detection of at least one target RNA in a sample of one or more cells, comprising: generating a cDNA complementary to an RNA in the sample; adding a ribonuclease to the sample to digest the RNA hybridized to the cDNA; contacting the sample with one or more padlock probes wherein the padlock probe(s) comprise terminal regions complementary to immediately adjacent regions on the cDNA and hybridizing the padlock probe to the cDNA at the complementary terminal regions; ligating the ends of the padlock probe(s); subjecting the circularized padlock probe(s) to rolling circle amplification (RCA); and detecting the rolling circle amplification product(s).

Some methods are provided for detecting a genetic mutation in a gene of a cell comprising: a) incubating the cell with a reverse transcriptase and a primer to hybridize the primer to RNA from the gene to generate a cDNA of all or part of the gene; b) incubating the cell with a ribonuclease under conditions to digest the RNA; c) incubating the cDNA with at least one padlock probe under conditions to hybridize the padlock probe to the cDNA, wherein the padlock probe comprises two terminal ends that are complementary to different but adjacent regions of the cDNA; d) incubating the cDNA and at least one padlock probe with a ligase under conditions to join terminal ends of the padlock probe; e) incubating the cDNA and the at least one ligated padlock probe with a polymerase and labeled nucleotides under conditions to amplify the at least one padlock probe and generate labeled, amplified padlock probes; and, f) assaying for one or more labeled nucleotides in the amplified probes to detect the genetic mutation.

In additional embodiments, there are methods for determining a nucleic acid sequence from a tissue section comprising: (a) generating a cDNA complementary to an RNA containing the nucleic acid sequence in the tissue section; (b) incubating the cDNA with a ribonuclease to the sample to digest the RNA; (c) hybridizing one or more padlock probes to the cDNA, wherein the padlock probe(s) comprise one or two terminal regions having the nucleic acid sequence; (d) incubating the hybridized padlock probes and cDNA with ligase under conditions to ligate the ends of the padlock probe(s); (e) incubating the replicating the padlock probe(s) using a polymerase to create an amplified product; and, (f) sequencing the complement of the nucleic acid sequence in the amplified product to determine the nucleic acid sequence and/or its complement.

In a further embodiment, there are methods for determining the presence and/or location of a genetic sequence in a cell in a biological sample comprising: (a) hybridizing a DNA complement having the genetic sequence to RNA; (b) digesting RNA hybridized to the DNA complement; (c) hybridizing a first padlock probe to at least a portion of the DNA complement, wherein the padlock probe comprises the genetic sequence on one of two terminal ends that are complementary to different but immediately adjacent regions of the DNA complement; (d) joining the two terminal ends of the padlock probe; and (e) replicating the circularized probe to yield a nucleic acid molecule comprising multiple copies of the replicated probe or subjecting the circularized probe to rolling circle amplification (RCA). In certain embodiments, methods also comprise (f) detecting the rolling circlue amplification products. In some embodiments, there is a step of detecting the presence or absence of the genetic sequence in the cell using a probe that hybridizes to the nucleic acid molecule. In certain aspects, the method further comprises generating the DNA complement that is hybridized to the RNA. In further embodiments, the two terminal ends of the padlock probe are joined using a ligase.

In another embodiment, methods for identifying a cell in a tissue sample that has a specific nucleic acid sequence are provided comprising: (a) incubating the cell with a DNA complement that includes the specific nucleic acid sequence to generate an RNA-DNA hybrid; (b) incubating the RNA target molecule with a ribonuclease under conditions to digest at least part of the RNA-DNA hybrid; (c) incubating the DNA complement with a padlock probe under conditions to hybridize the padlock probe to the DNA complement comprising the specific nucleic acid sequence, wherein the padlock probe comprises two terminal ends that are complementary to different but immediately adjacent regions of the DNA complement; (d) incubating the DNA complement and padlock probe with a ligase under conditions to join terminal ends of the padlock probe; (e) incubating the ligated padlock probe with a polymerase and nucleotides under conditions to prime replication of the padlock probe with the DNA complement and generate a nucleic acid with multiple copies of the replicated padlock probe; and (f) incubating the nucleic acid with multiple copies of the replicated padlock probe with one or more complementary oligonucleotides to detect the presence or absence of the specific sequence.

In one embodiment, there are methods for identifying a cell in a cell sample that has a specific nucleic acid sequence comprising: (a) incubating the cell sample with a ribonuclease-resistant primer that is immobilized to the sample and reverse transcriptase under conditions to generate a DNA complement of an RNA, wherein the DNA complement comprises the specific nucleic acid sequence; (b) incubating the cell sample with a ribonuclease under conditions to digest at least part of the RNA; (c) incubating the DNA complement with a padlock probe under conditions to hybridize the padlock probe to the DNA complement comprising the specific nucleic acid sequence, wherein the padlock probe comprises two terminal ends that are complementary to different but immediately adjacent regions of the DNA complement; (d) incubating the DNA complement and padlock probe with a ligase under conditions to join terminal ends of the padlock probe; (e) incubating the ligated padlock probe with a polymerase and nucleotides under conditions to prime replication of the padlock probe with the DNA complement and generate a nucleic acid with multiple copies of the replicated padlock probe; and (f) incubating the nucleic acid with multiple copies of the replicated padlock probe with one or more nucleic acid probes to detect the presence or absence of the specific sequence.

In another embodiment, methods are provided for in situ localization of a nucleic acid sequence in a cell in a biological sample on a slide comprising: (a) incubating an immobilized biological sample on solid support with reverse transcriptase and a ribonuclease-resistant primer under conditions to generate a nucleic acid molecule that contains the nucleic acid sequence and that hybridizes to a complementary RNA molecule in the cell to form an RNA-DNA hybrid; (b) adding a ribonuclease and incubating the ribonuclease under conditions to digest RNA in the RNA-DNA hybrid; (c) incubating the digested RNA-DNA hybrid under conditions to hybridize a complementing padlock probe to the DNA portion of the digested RNA-DNA hybrid, wherein the padlock probe comprises the nucleic acid sequence and has two terminal ends that are complementary to different but immediately adjacent regions of the DNA; (d) incubating the padlock probe hybridized to the DNA portion of the RNA-DNA hybrid with a ligase under conditions to ligate the terminal ends of the padlock probe; (e) incubating the ligated padlock probe with a polymerase and nucleotides under conditions to create a primer from the DNA that is used to replicate the padlock probe and generate a nucleic acid with multiple copies of the replicated padlock probe; and (f) incubating the nucleic acid with one or more complementing nucleic acid probes to detect the presence or absence of the specific sequence.

In specific embodiments of the methods for identifying a cell in a tissue sample, the methods for identifying a cell in a cell sample, or the methods for in situ localization of a nucleic acid sequence in a cell in a biological sample, e.g. as mentioned above, the sample is a formalin-fixed paraffin-embedded tissue section.

In another embodiment, there are methods for localized in situ detection of at least one RNA in a sample of cells, the methods comprising: (a) contacting the sample with a reverse transcriptase and a reverse transcriptase primer to generate cDNA from RNA in the sample; (b) adding a ribonuclease to the sample to digest the RNA hybridized to the cDNA; (c) contacting the sample with one or more padlock probes wherein the padlock probe(s) comprise terminal regions complementary to the cDNA and hybridizing the padlock probe(s) to the cDNA at the complementary terminal regions; (d) circularizing the padlock probe(s) by ligating, directly or indirectly, the ends of the padlock probe(s); (e) subjecting the circularized padlock probe(s) to rolling circle amplification (RCA) using a DNA polymerase having 3′-5′ exonuclease activity wherein, if necessary, the exonuclease activity digests the cDNA to generate a free 3′ end which acts as a primer for the RCA; and (f) detecting the rolling circle amplification product(s).

Methods of certain embodiments concern localizing or detecting in situ at least one target RNA in a sample of one or more cells, comprising: a) hybridizing the target RNA with a complementary nucleic acid that comprises a region complementary to the target RNA; b) digesting the RNA hybridized to the complementary nucleic acid; c) contacting the sample with one or more padlock probes, wherein the padlock probe(s) comprise terminal regions complementary to the cDNA and hybridizing the padlock probe to the cDNA at the complementary terminal regions; d) joining the ends of the padlock probe(s); and, e) subjecting the circularized padlock probe(s) to rolling circle amplification (RCA). In some embodiments, methods also involve generating the complementary nucleic acid while in others methods involve obtaining or providing the complementary nucleic acid. In some embodiments, methods further comprise sequencing all or part of one or more rolling circle amplification product(s).

The methods thus involve detecting the rolling circle amplification product (RCP) as a means of detecting the target RNA. The RCP is generated as a consequence of padlock probe recognition of a cDNA complementary to the target RNA (i.e. padlock probe binding to the cDNA complement of the target RNA by hybridization to complementary sequences in the cDNA) and ligation of the padlock probe to generate a circular template for the RCA reaction. The RCP may thus be viewed as a surrogate marker for the cDNA, which is detected to detect the RNA.

As discussed above, the method may be used for the detection of any RNA molecule type or RNA sequence present in a cell. In some embodiments, the method is used for the detection of mRNA. The cDNA complementary to the RNA in the sample may be generated by contacting the sample with an RNA-dependent DNA polymerase and a primer. The RNA dependent DNA polymerase may be, for example, a reverse transcriptase, such as an MMLV reverse transcriptase or an AMV reverse transcriptase.

In certain aspects, the primer used for first strand cDNA synthesis is ribonuclease resistant. A primer which is “ribonuclease resistant” means that it exhibits some (i.e, a measurable or detectable) degree of increased resistance to ribonuclease action (in particular to the action of an RNase H) over a naked, unmodified primer of the same sequence. Thus the primer is at least partially protected from digestion by the ribonuclease, or more particularly when the primer is hybridized to its RNA template, the primer/template hybrid is at least partially protected from ribonuclease digestion. In some embodiments at least 50% survives the ribonuclease treatment, while in further embodiments at least 60, 70, 80 or 90%, or even 100% survives the ribonuclease treatment. A primer may, for example, comprise 2′O-Me RNA, methylphosphonates or 2′ Fluor RNA bases, locked nucleic acid residues, or peptide nucleic acid residues, which make the primer resistant to digestion by ribonucleases.

In one embodiment, the primer comprises 2, 3, 4, 5, 6, 7, 8, 9 or more locked nucleic acids separated by 1 or more natural or synthetic nucleotides in the primer sequence. In certain embodiments, the primer comprises between 4 to 9 locked nucleic acids, with each locked nucleic acid being separated for the other locked nucleic acids by 1 or more natural or synthetic nucleotides in the primer sequence.

The term “reverse transcriptase primer” or “RT primer” as used herein (also known as a cDNA primer) refers to an oligonucleotide capable of acting as a point of initiation of cDNA synthesis by an RT under suitable conditions. Thus, a reverse transcription reaction is primed by an RT primer. The appropriate length of an RT primer typically ranges from 6 to 50 nucleotides or from 15 to 35 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the mRNA template, but may still be used. Shortening the primer from 30 to 25 nucleotides did not affect its function. A primer need not reflect the exact sequence of the template nucleic acid, but must be sufficiently complementary to hybridize with the template. The design of suitable primers for cDNA synthesis is well known in the art.

Typically, an RT primer is designed to bind to the region of interest in the RNA, for example a region within a particular RNA it is desired to detect, or a region within which sequence variations may occur (for example, allelic or splice variants, polymorphisms or mutations, etc., e.g. SNPs, etc.). Thus, in seeking to detect the presence or absence of particular mutations, etc. (e.g. in a genotyping context), the RT primer may be designed to bind in or around the region within which such mutations occur (e.g. near to such a region, for example within 100, 70, 50, 30, 20, 15, 10 or 5 nucleotides of such a region). Such mutations or sequence variations may be associated with disease (e.g. cancer) or disease risk or predisposition, or may with response to a therapeutic treatment, etc.

RT primers can incorporate additional features which allow for the immobilization of the primer to or within a cell in the sample but do not alter the basic property of the primer, that of acting as a point of initiation of cDNA synthesis. Thus it is contemplated that the primer may be provided with a functional moiety or means for immobilization of the primer to a cell or cellular component. This may for example be a moiety capable of binding to or reacting with a cell or cellular component and, as described above, such a cellular component may include RNA. Thus, the functional moiety may include a moiety(ies) which allow the primer to remain hybridized to the primer binding site within the template RNA, namely a moiety(ies) which render the primer resistant to ribonuclease digestion.

The primer may be modified to incorporate one or more reactive groups, e.g. chemical coupling agents, capable of covalent attachment to cells or cellular components. This may be achieved by providing the primer with chemical groups or modified nucleotide residues which carry chemical groups such as a thiol, hydroxy or amino group, a phosphate group via EDC (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride), NHS (N-hydroxysuccinimide)-esters, etc. which are reactive with cellular components such as proteins, etc. Such chemical coupling groups and means of introducing them into nucleic acid molecules are well known in the art. Potential reactive functionalities thus include nucleophilic functional groups (amines, alcohols, thiols, hydrazides), electrophilic functional groups (aldehydes, esters, vinyl ketones, epoxides, isocyanates, maleimides), functional groups capable of cycloaddition reactions, forming disulfide bonds, or binding to metals. Specific examples include primary and secondary amines, hydroxamic acids, N-hydroxysuccinimidyl esters, N-hydroxysuccinimidyl carbonates, oxycarbonylimidazoles, nitrophenylesters, trifluoroethyl esters, glycidyl ethers, vinylsulfones, and maleimides.

Alternatively or in addition, the primer may be provided with an affinity binding group capable of binding to a cell or cellular component or other sample component. Such an affinity binding group may be any such binding group known in the art which has specific binding activity for a corresponding binding partner in or on a cell, tissue, sample component, etc. Thus, representative binding groups include antibodies and their fragments and derivatives (e.g. single chain antibodies, etc.), other binding proteins, which may be natural or synthetic, and their fragments and derivatives, e.g. lectins, receptors, etc., binding partners obtained or identified by screening technology such as peptide or phage display, etc., aptamers and such like, or indeed small molecule binding partners for proteins e.g. for receptors and other proteins on or within cells. Such immobilization systems may work best in relation to cellular components which are abundant e.g. actin filaments.

The target RNA or the synthesized cDNA may be attached to a synthetic component in the sample, e.g. a synthetic gel matrix, instead of the native cellular matrix to preserve the localization of the detection signals. The cells or tissue may be immersed in a gel solution that upon polymerization will give rise to a gel matrix to which the cDNA or target can be attached. For example, if an Acrydite modification is included at the 5′ end of the cDNA primer, the cDNA can be covalently attached to a polyacrylamide matrix (Mitra and Church, 1999).

Alternatively or in addition to the aforementioned modifications to the RT primer, the modification described above may be used in which the 5′ phosphate of the primer may be linked to amines present on proteins in the cellular matrix via EDC-mediated conjugation, thus helping to maintain the localization of the RNA relative to other cellular components. Such a technique has previously been described in relation to microRNAs and their detection via in situ hybridization (Pena et al., 2009).

To ensure good ribonuclease resistance it may in certain instances be advantageous to use several modified residues in the RT primer, such as 2, 3, 4, 5 or 6 modified residues in a row for example. In some embodiments, modified residues may be incorporated into the RT primer every second, or every third, residue. In additional embodiments, the RT primer may comprise, comprise at least, or comprise at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more modified residues (or any range derivable therein). In the literature various modifications of nucleic acids that impart ribonuclease resistance have been described and any modification that prevents, or partially prevents, digestion of the RT primer or the RNA to which it is hybridized is encompassed in this method.

In one embodiment the modifications (e.g. modified residues) are placed at the 5′ end of the primer (in the 5′ region of the primer) and the 3′ end is left unmodified. For example, in some embodiments, at least or at most 1, 2, 3, 4, 5 or 6 residues from the 3′ end (or any range of derivable therein) are unmodified.

A preferred modification to confer ribonuclease resistance is the incorporation of LNA residues into the RT primer. Thus the RT primer may include at least 1 LNA residue and in certain embodiments include at least or at most 2, 3, 4, 5, 6, 7, 8 or 9 LNA residues (or any range derivable therein). As well conferring ribonuclease resistance, LNA monomers have enhanced hybridization affinity for complementary RNA, and thus may be used to enhance hybridization efficiency.

In a representative embodiment, the RT primer comprises LNA residues every second, or every third, residue. LNA is a bicyclic nucleotide analogue wherein a ribonucleoside is linked between the 2′-oxygen and the 4′-carbon atoms by a methylene unit. Primers comprising LNA exhibit good thermal stabilities towards complementary RNA, which permits good mismatch discrimination. Furthermore, LNA offers the possibility to adjust T_(m) values of primers and probes in multiplex assays.

The cDNA that is generated may be from 10 nucleotides to 1000 nucleotides in length, and in certain embodiments may range from 10 to 500 nucleotides in length including from 50 to 500 nucleotides in length, e.g., from 90 to 400 nucleotides in length, such as from 90 to 200 nucleotides in length, from 90 to 100 nucleotides in length, and so on. In certain representative embodiments, the cDNA may range in length from 10 to 100 nucleotides in length, from 30 to 90 nucleotides in length, from 14 to 70 nucleotides in length, from 50 to 80 nucleotides in length, and any length of integers between the stated ranges.

The cDNA may be made up of deoxyribonucleotides and/or synthetic nucleotide residues that are capable of participating in Watson-Crick-type or analogous base pair interactions. Thus the nucleotides used for incorporation in the reverse transcriptase step for synthesis of the cDNA may include any nucleotide analogue or derivative that is capable of participating in the reverse transcriptase reaction (i.e., capable of being incorporated by the reverse transcriptase).

Ribonucleases, also known as RNases, are a class of enzymes that catalyze the hydrolysis of RNA. A ribonuclease for use according to various embodiments will be able to degrade RNA in an RNA:DNA duplex. The RNases H are a family of ribonucleases that cleave the 3′-O—P-bond of RNA in a DNA:RNA duplex to produce 3′-hydroxyl and 5′-phosphate terminated products. Since RNase H specifically degrades the RNA in RNA:DNA hybrids and will not degrade DNA or unhybridized RNA it is commonly used to destroy the RNA template after first-strand cDNA synthesis by reverse transcription. RNase H thus represents a preferred class of enzymes for use. Members of the RNase H family can be found in nearly all organisms, from archaea and prokaryota to eukaryota. Again, suitable ribonuclease, particularly RNase H, enzymes are well-known and widely available.

Upon the hybridization of the terminal regions of a padlock probe to a complementary cDNA sequence, the padlock probe is “circularized” by ligation. The cirucularization of the padlock probe(s) may be carried out by ligating, directly or indirectly, the ends of the padlock probe(s). Procedures, reagents and conditions for this are well known and described in the art and may be selected according to choice. Suitable ligases include e.g., Tth DNA ligase, Taq DNA ligase, Thermococcus sp. (strain 9°N) DNA ligase (9°N™ DNA ligase, New England Biolabs), Ampligase™ (Epicentre Biotechnologies) and T4 DNA ligase. In specific embodiments, the in the cirucularization of the padlock probe(s) step, the terminal regions of the padlock probe may hybridize to non-contiguous regions of the cDNA such that there is a gap between the terminal regions. In further specific embodiments of this method, the gap may be a gap of 1 to 60 nucleotides, such as a gap of 1 to 40 nucleotides or a gap of 3 to 40 nucleotides. In specific embodiments, the gap may be a gap of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 35, 37, 40, 42, 45, 47, 50, 52, 55, 57 or 60 nucleotides, of any integer of nucleotides in between the indicated values. In further embodiments, the gap may be larger than 60 nucleotides. In further embodiments, the gap may have a size of more than 60 nucleotides. In further embodiments, the gap between the terminal regions may be filled by a gap oligonucleotide or by extending the 3′ end of the padlock probe. The gap oligonucleotide may accordingly have a size of 1 to 60 nucleotides, e.g. a size of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 35, 37, 40, 42, 45, 47, 50, 52, 55, 57 or 60 nucleotides, or any integer of nucleotides in between the indicated values. In further embodiments, the size of the gap oligonucleotide may be more than 60 nucleotides.

Rolling circle amplification or “RCA” of the circularized padlock probe results in the synthesis of a concatemeric amplification product containing numerous tandem repeats of the probe nucleotide sequence. RCA reactions and the conditions therefor are widely described in the literature and any such conditions, etc. may be used, as appropriate. The ligation reaction may be carried out at the same time (i.e. simultaneously) as the RCA reaction of step, i.e. in the same step. In some embodiments, the RCA reaction is primed by the 3′ end of the cDNA strand to which the padlock probe has hybridized. In other embodiments, instead of priming the RCA reaction with the 3′ end of the cDNA, a primer is hybridized to the padlock probe and primes the RCA reaction. In certain aspects, this primer hybridizes to a region of the padlock probe other than the 5′ and 3′ terminal regions of the padlock probe.

Where the RCA reaction is primed by the 3′ end of the cDNA strand to which the padlock probe has hybridized, any unpaired 3′ nucleotides in the cDNA are removed in order to generate the primer for RCA. This may be achieved by using a polymerase having 3′-5′ exonuclease activity. Such target-primed RCA procedures are known and described in the art as are appropriate polymerase enzymes for such use. Thus, for example, a DNA polymerase such phi29 (φ29) polymerase, Klenow fragment, Bacillus stearothermophilus DNA polymerase (BST), T4 DNA polymerase, T7 DNA polymerase, or DNA polymerase I may be used. The skilled person may readily determine other suitable polymerases which might be used, including, for example, DNA polymerases that have been engineered or mutated to have desirable characteristics. In the RCA reaction, the polymerase thus extends the 3′ end of the cDNA using the circularized padlock probe as template. As a result of RCA, concatemeric amplification products containing numerous tandem repeats of the probe nucleotide sequence are produced and may be detected as indicative of the presence and/or nature of a RNA in the sample. Alternatively, a separate enzyme having 3′-5′ exonuclease activity may be added to the reaction to generate the free 3′ end, in which case a DNA polymerase lacking 3′-5′ exonuclease activity could then be used for RCA. In some cases, depending on the proximity of the hybridized padlock probe to the 3′ end of the target cDNA, it may not be necessary to digest the cDNA to generate a free 3′ end at the appropriate position for it to act as a primer for RCA.

In various methods described herein, there may be one or more wash steps. Multiple washes may be employed at one or more points during a process. On certain embodiments there are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more wash steps (and any range derivable therein) in a method. Each wash may involve the same or different washing reagents depending on the purpose for the wash.

The terms “padlock probe” and “probe” and their plural forms are synonymous and are used interchangeably throughout this specification. The use of a single padlock probe occurs in the case of a “simplex” (as opposed to “multiplex”) embodiment of the method, i.e. when a single RNA or a single variant in a RNA are to be detected. It will be understood that the term “single” as used in relation to a padlock probe, or the RNA, means single in the sense of a “single species,” i.e. a plurality of RNA molecules of the same type may be present in the sample for detection, and a plurality of identical padlock probes specific for that RNA may be used, but such pluralities relate only to a unique sequence of RNA or padlock probe. In multiplex embodiments, two or more different target RNAs are to be detected in a sample of cells. In such embodiments, the sample of cells is contacted with a plurality of padlock probes for each target RNA, such that the number of probes contacted with the sample may be two or more, e.g., three or more, four or more, etc. Optionally, up to 10, 15 or 20 probes may be used. Such methods find particular use in high-throughput applications. For example, the method may employ or may employ at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40, or any range derivable therein, padlock probes in a single reaction.

For example, in one embodiment, the method comprises contacting the sample with at least a first and a second padlock probe, wherein the first padlock probe comprises terminal regions complementary to immediately adjacent regions on the cDNA, and wherein the second padlock probe comprises terminal regions that differ from the terminal regions of the first padlock probe only by a single nucleotide at the 5′ or 3′ terminus of the second padlock probe. In this manner, the two padlock probes can be used to detect a single nucleotide differences in an RNA sequence. For example, the first padlock probe may be configured to hybridize to a cDNA complementary to a wild-type mRNA sequence, and the second padlock probe is configured to hybridize to a cDNA complementary to a single nucleotide variant of the mRNA sequence. In addition to detecting nucleic acid substitutions, the padlock probes may be configured to detect insertions or deletions in a nucleic acid sequence.

The padlock probe may be of any suitable length to act as an RCA template. For example, the padlock probe may have an overall length (including two arms and a backpiece) of between 50 and 150 nucleotides, of between 60 to 120 nucleotides, or of between 70 to 100 nucleotides. Thus, the padlock probe may have, for instance, a length of, of at least, or of at most 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 nucleotides, or any range derivable therein. The arms of the padlock probes may have any suitable length, e.g. each may have a length of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, e.g. 13, 24, 25, 26, 27, 28, 29, 30, 32, 35, 36, 37, 38, 39 or 40 nucleotides, or any range derivable therein. The length of the two arms of the padlock probes may, in certain embodiments, be identical or essentially identical, e.g. showing a length difference of 1-2 nucleotides. In further embodiments, the length of the two arms may differ one from the other by more than 2 nucleotides, e.g. one arm having a length of 15 nucleotides, whereas the other having a length of 20 nucleotides. The length difference in some embodiments may not surpass 5 to 7 nucleotides. In addition to the end regions, which are complementary to the cDNA, the probe may contain features or sequences or portions useful in RCA or in the detection or further amplification of the RCA product. Such sequences may include binding sites for an RCA primer, hybridization probes, and/or amplification or sequencing primers. Thus, a padlock probe may be viewed as having a “back piece” which links the 3′ and 5′ target-complementary regions. By including within this back piece or linking region a particular sequence, to which when amplified by RCA of the circularized probe, a detection probe or primer may bind in the RCP, the padlock probe may be seen as having, or more particularly as providing, a detection site for detection of the RCP. Accordingly, the padlock probe may contain an arbitrary “tag” or “barcode” sequence which may be used diagnostically to identify the cDNA, and by extension the corresponding mRNA, to which a given RCA product relates, in the context of a multiplex assay. Such a sequence is simply a stretch of nucleotides comprising a sequence designed to be present only in the padlock probe which is “specific for” (i.e. capable of hybridizing only to) a particular cDNA. Thus, for example in the context of padlock probes for genotyping, the tag sequence (or detection site) may be different for the padlock probes designed to detect the wild-type sequence and the mutant(s)/sequence variant(s) thereof.

In certain embodiments, a detection probe that is complementary to the backbone sequence of a padlock probe may be labeled or tagged. In some embodiments, the detection probe has a substance attached to it that can be detected directly or indirectly. In further embodiments, the substance attached to the detection probe is or contains an epitope for an antibody or antibody fragment. In certain embodiments, the substance is or comprises a hapten. Therefore, in some methods provided herein, a detection probe is recognized by an antibody or antibody fragment. Detection of the rolling circle amplification product may involve detection of the antibody or antibody fragment directly or indirectly. A direct method might involve the use of an antibody is itself is labeled with a detectable moiety. Alternatively, detection of the antibody of antibody fragment may involve a secondary antibody that is specific for the antibody or antibody fragment that binds the substance on the detection probe.

A padlock probe may have ends that can be joined when juxtaposed with one another upon hybridization of a complementing nucleic acid. The ends may be chemically or enzymatically joined. In some embodiments, ends are joined by ligating the ends using a ligase.

In certain aspects, the padlock probes comprise a “tag” or “detection probe binding region.” The detection probe binding region may be used to incorporate detection probe binding regions into the rolling circle amplification products for subsequent hybridization to labeled detection probes. Different padlock probes may have different detection probe binding regions such that differentially labeled detection probes may be used in the detection of the rolling circle amplification products. For example, a first padlock probe may comprise a first detection probe binding region, and a second padlock probe may comprise a second detection probe binding region. The sample may then be contacted with a first labeled detection probe comprising a sequence identical to the first detection probe binding region of the first padlock probe, and a second labeled detection probe comprising a sequence identical to the second detection probe binding region of the first padlock probe, such that the first and second labeled detection probes hybridize to the rolling circle amplification products, if any, generated by the first and second padlock probes.

The term “detection” is used broadly herein to include any means of determining, or measuring (e.g. quantitatively determining), the presence of at least one RNA (i.e. if, or to what extent, it is present, or not) in the sample. “Localized” detection means that the signal giving rise to the detection of the RNA is localized to the RNA. The RNA may therefore be detected in or at its location in the sample. In other words the spatial position (or localization) of the RNA within the sample may be determined (or “detected”). This means that the RNA may be localized to, or within, the cell in which it is expressed or to a position within the cell or tissue sample. Thus “localized detection” may include determining, measuring, assessing or assaying the presence or amount and location, or absence, of RNA in any way. Quantitative and qualitative determinations, measurements or assessments are included, including semi-quantitative. Such determinations, measurements or assessments may be relative, for example when two or more different RNAs in a sample are being detected. In certain embodiments, a detection probe is labelled. In some embodiments, a labeled detection or padlock probe comprises one or more fluorescent labels, enzymatic labels, chromogenic labels, radioactive labels, luminescent labels, magnetic labels, or electron-density labels. In particular embodiments, one or more probes that are differentially labeled with respect to one another may be employed or included in methods or kits discussed herein.

In some embodiments, a rolling circle amplification product or replicated circularized padlock probe is labeled directly. In some embodiments, methods involve subjecting the circularized padlock probe(s) to rolling circle amplification by adding labeled nucleotides to generate labeled, amplified padlock(s). In some embodiments, at least two different padlock probes are used. In further aspects, the at least two different padlock probes have different backbone sequences. It is contemplated that in some cases a difference in backbone sequence comprises a difference in nucleotide content. In particular embodiments, at least two differentially labelled nucleotides are employed. In some cases, at least two different padlock probes are used and the amplified padlock probes are differentially labeled. The term “backbone sequence” refers to the contiguous sequence in the padlock probe that is not complementary to the target sequence. The backbone sequence lies between the two arms of a padlock probe that are complementary to a target sequence.

In some embodiments, there may be at least two padlock probes that have different backbone sequences. In some instances, a difference between backbone sequences comprises a difference in nucleotide content by at least 2×. For example, one backbone may have at least twice as many of a specific nucleotide as the other backbone. The nucleotide content of G, A, T, or C may vary between padlock probes such that they can be distinguished from one another. In one embodiment, a difference in the nucleotide content comprises a difference in the number of guanines or G nucleotides in the backbone sequence. In another embodiment a difference in the nucleotide content comprises a difference in the number of adenines or A nucleotides in the backbone sequence. In another embodiment a difference in the nucleotide content comprises a difference in the number of thymidine or T nucleotides in the backbone sequence. In another embodiment a difference in the nucleotide content comprises a difference in the number of cytosine or C nucleotides in the backbone sequence. In certain cases, a backbone sequence does not have at least one of the four nucleotides (G, A, T, or C). In further examples, one of the padlock probes is missing at least one of G, A, T, or Cs, and another padlock probe is also missing at least one of G, A, T, or Cs; the two can be distinguished if they differ by which nucleotide each is missing. In further embodiments, four different padlock probes that each lack a different nucleotide may be employed.

In other embodiments, rolling circle amplification product(s) are detected by sequentially adding at least two probes. In some cases, each probe is detected prior to the addition of a next probe. Methods may involve eliminating what is detected prior to the addition of the next probe, where “eliminating” means a level of detection that is at or below background levels of detection. In some cases, this may involve photobleaching.

In some embodiments, rolling circle amplification product(s) are detected with one or more probes that comprises one or more branches having one or more labeling moieties on each branch. These branched probes increase signal that can be detected.

As used herein, the term “in situ” refers to the detection of at least one RNA in its native context, i.e. in the cell, bodily fluid, or tissue in which it normally occurs. Thus, this may refer to the natural or native localization of an RNA. In other words, the RNA may be detected where, or as, it occurs in its native environment or situation. Thus, the RNA is not moved from its normal location, i.e. it is not isolated or purified in any way, or transferred to another location or medium, etc. Typically, this term refers to the RNA as it occurs within a cell or within a cell, organ, bodily fluid, or tissue sample, e.g. its native localization within the cell or tissue and/or within its normal or native cellular environment. In certain embodiments, a sample is on a solid support. The solid support may be a slide, a bead, an array, or chip. This is in contrast to a sample in solution, such as in a tube. In certain embodiments, the solid support is a slide, which may or may not have a cover, such as a coverslip or covertile.

In certain embodiments, methods may also involve a sample that is stained or a sample that is stained during or after contact with one or more padlock probes. In specific embodiments, a sample, such as cells or tissue, is stained prior to contact with one or more padlock probes. In particular embodiments, a sample is stained with hematoxylin and eosin.

A variety of labels are known for labeling nucleic acids and may be used in the detection of rolling circle amplification products. Non-limiting examples of such labels include fluorescent labels, chromogenic labels, radioactive labels, luminescent labels, magnetic labels, and electron-density labels. Labels may be incorporated directly into the amplification product, such as with modified or labeled dNTPs during amplification. Alternatively, the amplification products may be labeled indirectly, such as by hybridization to labeled probes. In multiplex reactions, it is contemplated that a different label may be used for each different amplification product that may be present in the reaction.

The method of detection will depend on the type of label used. In certain embodiments, the detection is by imaging or direct visualization of fluorescent or chromogenic labels. Accordingly, the present method allows for the detection of the amplification products in situ at the location of the target RNA. This sensitivity permits, for example, genotyping at the single-cell level.

In certain embodiments, methods will also include incubating the amplification product with a detection probe under conditions to allow hybridization between the product and the probe. In some embodiments, the detection probe has one or more fluorescent labels, enzymatic labels, epitope labels, chromogenic labels, radioactive labels, luminescent labels, magnetic labels, or electron-density labels. Furthermore, methods may also include incubating the detection probe with one or more polypeptides that binds the one or more labels. In some situations, at least one or more polypeptides is an antibody. It is further contemplated that methods may also involve incubating the one or more polypeptides that binds the one or more labels with a secondary polypeptide that binds the label-binding polypeptide. In some instances, the secondary polypeptide is an antibody. Furthermore, some methods involve a label-binding polypeptide or a secondary polypeptide that comprises a detectable label. Additional embodiments, involve detecting the rolling circle amplification product(s), which may be achieved by steps that include assaying for the label(s) on the detection probe. In certain embodiments, methods also involve incubating the rolling circle amplification product(s) and label(s) on the probe with an enzyme substrate to detect the rolling circle amplification product(s).

In certain embodiments, following rolling circle amplification or replication of a circularized padlock probe, resulting nucleic acid molecules such as rolling circle amplification products or replicated circularized padlock probes may be sequenced. All or part of the products or probes may be sequenced. In certain embodiments, the identity of a single nucleotide in the RCA product or replicated circularized probe may be determined. In certain embodiments, the identity is determined by sequencing that position or nucleotide.

The “sample” may be any sample of cells in which an RNA molecule may occur, to the extent that such a sample is amenable to in situ detection. Typically, the sample may be any biological, clinical or environmental sample in which the RNA may occur, and particularly a sample in which the RNA is present at a fixed, detectable or visualizable position in the sample. The sample will thus be any sample which reflects the normal or native (in situ) localization of the RNA, i.e. any sample in which it normally or natively occurs. The sample may, for example, be derived from a tissue or organ of the body, or from a bodily fluid. Such a sample will advantageously be or comprise a cell or group of cells such as a tissue. The sample may, for example, be a colon, lung, pancreas, prostate, skin, thyroid, liver, ovary, endometrium, kidney, brain, testis, lymphatic fluid, blood, plasma, urinary bladder, or breast sample, or comprise colon, lung, pancreas, prostate, skin, thyroid, liver, ovary, endometrium, kidney, brain, testis, lymphatic fluid, blood, urinary bladder, or breast cells, groups of cells or tissue portions.

Particularly preferred are samples such as cultured or harvested or biopsied cell or tissue samples, e.g., as mentioned above, in which the RNA may be detected to reveal the qualitative nature of the RNA, i.e. that it is present, or the nucleotide sequence of the mRNA or the presence and/or identity of one or more nucleotides in the mRNA, and localization relative to other features of the cell. The sample of cells may be freshly prepared or may be prior-treated in any convenient way such as by fixation or freezing. Accordingly, fresh, frozen or fixed cells or tissues may be used, e.g. FFPE tissue (Formalin Fixed Paraffin Embedded).

In specific embodiments, the sample of cells or tissues may be prepared, e.g. freshly prepared, or may be prior-treated in any convenient way, with the proviso that the preparation is not a preparation of fresh frozen tissues. In further specific embodiments, the sample of cells or tissues may be prepared, e.g. freshly prepared, or may be prior-treated in any convenient way, with the proviso that the preparation is not a preparation including seeding on Superfrost Plus slides. In yet additional specific embodiments, the sample of cells or tissues may be prepared, e.g. freshly prepared, or may be prior-treated in any convenient way, with the proviso that the preparation is not a preparation as disclosed in Larsson et al., Nature Methods, 2010, Vol 7 (5), pages 395-397. In very specific embodiments, the sample of cells or tissues may be prepared, e.g. freshly prepared, or may be prior-treated in any convenient way, with the proviso that the preparation is not a preparation as disclosed in section “Preparation of tissue sections” and/or “Sample pretreatment for in situ experiments” of Online methods of Larsson et al., Nature Methods, 2010, Vol 7 (5), pages 395-397.

Thus, tissue sections, treated or untreated, may be used. Alternatively a touch imprint sample of a tissue may be used. In this procedure a single layer of cells is printed onto a surface (e.g. a slide) and the morphology is similar to normal tissue sections. The touch imprint are obtained using fresh tissue sample. Other cytological preparations may be used, e.g. cells immobilized or grown on slides, or cell prepared for flow cytometry. In specific embodiments, the sample of cells or tissues may be prepared, e.g. freshly prepared, or may be prior-treated in any convenient way. In certain embodiments, the sample comprises fixed tissue. In some aspects, the sample is fixed with an alcohol, ketone, aldehyde, glycol or mixture thereof.

The sample may comprise any cell type that contains RNA including all types of mammalian and non-mammalian animal cells, plant cells, algae including blue-green algae, fungi, bacteria, protozoa, etc. Representative samples thus include clinical samples, e.g. whole blood and blood-derived products, blood cells, tissues, biopsies, as well as other samples such as cell cultures and cell suspensions, etc. In certain aspects, the sample contains, or is suspected of containing, cancer cells, such as colorectal cancer or lung cancer cells, pancreas cancer, prostate cancer, skin cancer, thyroid cancer, liver cancer, ovary cancer, endometrium cancer, kidney cancer, cancer of the brain, testis cancer, acute non lymphocytic leukemia, myelodysplasia, urinary bladder cancer, head and neck cancer or breast cancer cells. For example, the sample may be a colon, lung, pancreas, prostate, skin, thyroid, liver, ovary, endometrium, kidney, brain, testis, lymphatic fluid, blood, plasma, urinary bladder, or breast sample suspected to be cancerous, or suspected to comprise an mRNA found in a cancer or cancerous cell, or cancerous cell group or tissue.

In some embodiments, a sample is obtained from a patient who previously was known to have cancer, which was treated or went into remission. In some cases, the patient may have a recurrent cancer. In other embodiments, the patient may have a metastasis or be suspected of having a metastasis or be at risk for metastasis. A patient at risk for cancer or metastasis may be at risk because of familial history or at determination of other genetic predispositions. In other embodiments, the patient may have been determined or may be determined to have cells exhibiting the pathology of cancer or precancer cells.

Cancer “recurrence,” in pathology nomenclature, refers to cancer re-growth at the site of the primary tumor. For many cancers, such recurrence results from incomplete surgical removal or from micrometastatic lesions in neighboring blood or lymphatic vessels outside of the surgical field. Conversely, “metastasis” refers to a cancer growth distant from the site of the primary tumor. Metastasis of a cancer is believed to result from vascular and/or lymphatic permeation and spread of tumor cells from the site of the primary tumor prior to surgical removal. The prevailing clinical nomenclature used for cancer statistics is somewhat confusing in that patients who experience a second episode of a treated cancer are referred to as having undergone a “recurrence”, whereas these lesions are usually temporally remote metastases at sites distant from the primary cancer. This clinical terminology will be used herein, i.e., the term “recurrence” denotes these late-arising metastatic lesions, unless specific pathologic nomenclature is needed to separate the two forms of clinical recurrence.

In certain embodiments, the sample contains pre-cancerous or premalignant cells, including but not limited to metaplasias, dysplasias, and/or hyperplasias. It may also be used to identify undesirable but benign cells, such as squamous metaplasia, dysplasia, benign prostate hyperplasia cells, and/or hyperplastic lesions.

In additional embodiments, methods and compositions are implemented with respect to a specific type of lung cancer. They may be implemented with patients diagnosed, at risk for, or exhibiting symptoms of a specific type of lung cancer. In some embodiments, the specific type of lung cancer is non-small cell lung cancer (NSCLC) as distinguished from small cell lung cancer (SCLC). In other embodiments, the NSCLC is squamous cell carcinoma (or epidermoid carcinoma), adenocarcinoma, bronchioalveolar carcinoma, or large-cell undifferentiated carcinoma.

In certain embodiments, methods and compositions are implemented with respect to a specific type of colon cancer. They may be implemented with patients diagnosed, at risk for, or exhibiting symptoms of a specific type of colon cancer. In some embodiments, the specific type of colon cancer is an adenocarcinoma, leiomyosarcoma, colorectal lymphoma, melanoma, neuroendocrine tumors (aggressive or indolent). In the case of adenocarcinomas, the cancer may be further subtyped into mucinous or signet ring cell.

The terms “target, “target sequence”, “target region”, and “target nucleic acid,” etc. are used synonymously herein and refer to the nucleic acid, or to a region or sequence thereof, which is to be detected or to which a reagent used in the method binds, for example the RNA to be detected, or the cDNA, or more particularly the regions thereof, to which the padlock probe is hybridized. Thus a target sequence may be within a cDNA, in which case it is to be understood that the cDNA nucleotide sequence is derived from and is complementary to the target RNA nucleotide sequence. The target may, in certain embodiments, be a single RNA molecule. In other embodiments, the target may be at least one RNA molecule, e.g. a group of 2, 3, 4, 5, 6 or more RNA molecules. These RNA molecules may differ in molecule type, and/or may differ in sequence.

The term “hybridization,” as used herein, refers to the formation of a duplex structure by two single-stranded nucleic acids due to complementary base pairing. Hybridization can occur between fully complementary nucleic acid strands or between “substantially complementary” nucleic acid strands that contain minor regions of mismatch. Conditions under which hybridization of fully complementary nucleic acid strands is strongly preferred are referred to as “stringent hybridization conditions” or “sequence-specific hybridization conditions”. Stable duplexes of substantially complementary sequences can be achieved under less stringent hybridization conditions; the degree of mismatch tolerated can be controlled by suitable adjustment of the hybridization conditions. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length and base pair composition of the oligonucleotides, ionic strength, and incidence of mismatched base pairs, following the guidance provided by the art (see, e.g., Sambrook et al., 1989; Wetmur, 1991; Owczarzy et al., 2008, which are incorporated herein by reference). Thus the design of appropriate primers and probes, and the conditions under which they hybridize to their respective targets is well within the routine skill of the person skilled in the art.

Mutations in KRAS are common in several types of cancer. In certain embodiments, methods are provided for detecting the presence or absence of KRAS mutations in situ. In particular embodiments, the method uses padlock probe(s) configured to hybridize to cDNA(s) corresponding to one or more mutant KRAS mRNA sequences selected from the group consisting of 12AGT, 12CGT, 12TGT, 12GAT, 12GCT, 12GTT, and 13GAC (wherein the wild-type sequence is 12GGT and 13GGC) and mutants of KRAS codon 61, mutants of KRAS codon 146, and mutants of the 3′ untranslated region of KRAS. In certain embodiments, the method uses padlock probe(s) configured to hybridize to cDNA(s) corresponding to the wild-type KRAS sequence. In further embodiments, the method uses padlock probe(s) configured to hybridize to cDNA(s) corresponding to one or more mutant KRAS mRNA sequences selected from the group consisting of 12AGT, 12CGT, 12TGT, 12GAT, 12GCT, 12GTT, and 13GAC (wherein the wild-type sequence is 12GGT and 13GGC) and mutants of KRAS codon 61, mutants of KRAS codon 146, and mutants of the 3′ untranslated region of KRAS; and to one or more wild-type KRAS mRNA sequences selected from the group consisting of 12GGT and 13GGC, wild-type sequences of KRAS codon 61, KRAS codon 146, and of the 3′ untranslated region of KRAS.

In another embodiment, methods are provided for detecting the presence or absence of mutations in mRNA that codes for HER2, cMyc, TERT, APC, Braf, PTEN, PI3K, and/or EGFR. In particular embodiments, the method uses padlock probe(s) configured to hybridize to cDNA(s) corresponding to one or more mutant HER2, cMyc, TERT, Braf, APC, PTEN and/or PI3K mRNA sequences. In further embodiments, the method uses padlock probe(s) configured to hybridize to cDNA(s) corresponding to one or more wild-type HER2, cMyc, TERT, Braf, APC, PTEN and/or PI3K mRNA sequences. In further embodiments, padlock probe(s) are configured to hybridize to cDNA(s) corresponding to one or more mutant Braf, PTEN and/or PI3K mRNA sequences, and to one or more wild-type Braf, APC, PTEN and/or PI3K mRNA sequences. Accordingly methods are provided for detecting the presence or absence of a rolling circle amplification product corresponding to one or more of mutant and wild-type Braf, APC, PTEN and/or PI3K mRNA sequences.

In yet another group of embodiments, the padlock probe(s) are configured to hybridize to cDNA(s) corresponding to one or more mutant KRAS mRNA sequences and to one or more mutant Braf mRNA sequences; or to one or more mutant KRAS mRNA sequences and to one or more mutant APC mRNA sequences; or to one or more mutant KRAS mRNA sequences and to one or more mutant PTEN mRNA sequences; or to one or more mutant KRAS mRNA sequences and to one or more mutant PI3K mRNA sequences. Embodiments accordingly provide methods for detecting the presence or absence of a rolling circle amplification product corresponding to mutant KRAS and mutant Braf mRNA sequences; or corresponding to mutant KRAS and mutant APC mRNA sequences; or corresponding to mutant KRAS and mutant PTEN mRNA sequences; or corresponding to mutant KRAS and mutant PI3K mRNA sequences.

In further embodiments, the padlock probe(s) are configured to hybridize to cDNA(s) corresponding to wild-type KRAS and wild-type Braf mRNA sequences; or corresponding to wild-type KRAS and wild-type APC mRNA sequences; or corresponding to wild-type KRAS and wild-type PTEN mRNA sequences; or corresponding to wild-type KRAS and wild-type PI3K mRNA sequences. Accordingly methods are provided for detecting the presence or absence of a rolling circle amplification product corresponding to wild-type KRAS and Braf mRNA sequences; or corresponding to wild-type KRAS and APC mRNA sequences; or corresponding to wild-type KRAS and PTEN mRNA sequences; or corresponding to wild-type KRAS and PI3K mRNA sequences.

In a further group of embodiments, the padlock probe(s) are configured to hybridize to cDNA(s) (i) corresponding to one or more mutant KRAS mRNA sequences and to one or more mutant Braf mRNA sequences; or corresponding to one or more mutant KRAS mRNA sequences and to one or more mutant APC mRNA sequences; or corresponding to one or more mutant KRAS mRNA sequences and to one or more mutant PTEN mRNA sequences; or corresponding to one or more mutant KRAS mRNA sequences and to one or more mutant PI3K mRNA sequences; and (ii) corresponding to wild-type KRAS and Braf mRNA sequences; or corresponding to wild-type KRAS and APC mRNA sequences; or corresponding to wild-type KRAS and PTEN mRNA sequences; or corresponding to wild-type KRAS and PI3K mRNA sequences. Methods are provided for detecting the presence or absence of a rolling circle amplification product corresponding to one or more mutant and wild-type KRAS and Braf mRNA sequences; or corresponding to one or more mutant and wild-type KRAS and APC mRNA sequences; or corresponding to one or more mutant and wild-type KRAS and PTEN mRNA sequences; or corresponding to one or more mutant and wild-type KRAS and PI3K mRNA sequences.

One embodiment provides a collection of padlock probes specific for mutations to the KRAS gene, comprising:

(a) Y1-X1-Z1-A

(b) Y1-X1-Z1-T

(c) Y1-X1-Z1-C

(d) Y2-X1-Z2-A

(e) Y2-X1-Z2-T

(f) Y2-X1-Z2-C, and

(g) Y3-X1-Z3-A;

where:

X1 is from 5-50 nucleotides;

Y1+Z1=20 to 40 nucleotides;

Y2+Z2=20 to 40 nucleotides;

Y3+Z3=20 to 40 nucleotides;

Y1 is GTGGCGTAGGCAAGA (SEQ ID NO:1), GTGGCGTAGGCAAG (SEQ ID NO:2), GTGGCGTAGGCAA (SEQ ID NO:3), GTGGCGTAGGCA (SEQ ID NO:4), GTGGCGTAGGC (SEQ ID NO:5), GTGGCGTAGG (SEQ ID NO:6), GTGGCGTAG, GTGGCGTA, GTGGCGT, GTGGCG, GTGGC, GTGG, GTG, GT, G;

Y2 is TGGCGTAGGCAAGAG (SEQ ID NO:7), TGGCGTAGGCAAGA (SEQ ID NO:8), TGGCGTAGGCAAG (SEQ ID NO:9), TGGCGTAGGCAA (SEQ ID NO:10), TGGCGTAGGCA (SEQ ID NO:11), TGGCGTAGGC (SEQ ID NO:12), TGGCGTAGG, TGGCGTAG, TGGCGTA, TGGCGT, TGGCG, TGGC, TGG, TG, T;

Y3 is TGGCGTAGGCAAGAGTGC (SEQ ID NO:13), TGGCGTAGGCAAGAGTG (SEQ ID NO:14), TGGCGTAGGCAAGAGT (SEQ ID NO:15), TGGCGTAGGCAAGAG (SEQ ID NO:7), TGGCGTAGGCAAGA (SEQ ID NO:8), TGGCGTAGGCAAG (SEQ ID NO:9), TGGCGTAGGCAA (SEQ ID NO:10), TGGCGTAGGCA (SEQ ID NO:11), TGGCGTAGGC (SEQ ID NO:12), TGGCGTAGG, TGGCGTAG, TGGCGTA, TGGCGT, TGGCG, TGGC, TGG, TG, T; Z1 is TGGTAGTTGGAGCT (SEQ ID NO:27), GGTAGTTGGAGCT (SEQ ID NO:28), GTAGTTGGAGCT (SEQ ID NO:29), TAGTTGGAGCT (SEQ ID NO:30), AGTTGGAGCT (SEQ ID NO:31), GTTGGAGCT, TTGGAGCT, TGGAGCT, GGAGCT, GAGCT, AGCT, GCT, CT, T, or a bond; Z2 is GGTAGTTGGAGCTG (SEQ ID NO:16), GTAGTTGGAGCTG (SEQ ID NO:17), TAGTTGGAGCTG (SEQ ID NO:18), AGTTGGAGCTG (SEQ ID NO:19), GTTGGAGCTG (SEQ ID NO:20), TTGGAGCTG, TGGAGCTG, GGAGCTG, GAGCTG, AGCTG, GCTG, CTG, TG, G or a bond; and Z3 is AGTTGGAGCTGGTG (SEQ ID NO:21), GTTGGAGCTGGTG (SEQ ID NO:22), TTGGAGCTGGTG (SEQ ID NO:23), TGGAGCTGGTG (SEQ ID NO:24), GGAGCTGGTG (SEQ ID NO:25), GAGCTGGTG (SEQ ID NO:26), AGCTGGTG, GCTGGTG, CTGGTG, TGGTG, GGTG, GGTG, GTG, TG, G or a bond.

In some embodiments, the collection of KRAS probes, further comprises:

(h) Y1-X2-Z1-G

(i) Y2-X2-Z2-G

(j) Y3-X2-Z3-G

where X2 is from 10-50 nucleotides and differs from X1.

In a specific embodiment, the collection of KRAS probes, further comprises:

(h) Y1-X2-Z1-G

(i) Y2-X2-Z2-G

(j) Y3-X2-Z3-G

where X2 is from 10-50 nucleotides and differs from X1.

Further embodiments provide a collection of padlock probes specific for mutations to the Braf gene comprising:

(k) Y1-X1-Z1-A

where:

X1 is from 5-50 nucleotides;

Y1+Z1=20 to 40 nucleotides;

Y1 is GAAATCTCGATGGAG (SEQ ID NO:102), AAATCTCGATGGAG (SEQ ID NO:103), AATCTCGATGGAG (SEQ ID NO:104), ATCTCGATGGAG (SEQ ID NO:105), TCTCGATGGAG (SEQ ID NO:106), CTCGATGGAG (SEQ ID NO:107), TCGATGGAG, CGATGGAG, GATGGAG, ATGGAG, TGGAG, GGAG, GAG, AG, G; and

Z1 is TGGTCTAGCTACAG (SEQ ID NO:108), GGTCTAGCTACAG (SEQ ID NO:109), GTCTAGCTACAG (SEQ ID NO:110), TCTAGCTACAG (SEQ ID NO:111), CTAGCTACAG (SEQ ID NO:112), TAGCTACAG, AGCTACAG, GCTACAG, CTACAG, TACAG, ACAG, CAG, AG, G, or a bond.

In some embodiments, the collection of Braf probes further comprises:

(l) Y1-X2-Z1-T

where X2 is from 10-50 nucleotides.

In a specific embodiment, the collection of Braf probes further comprises:

(l) Y1-X2-Z1-T

where X2 is from 10-50 nucleotides and differs from X1.

Further embodiments provide a collection of padlock probes specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, comprising:

(m) Y1-X1-Z1-W

where:

X1 is from 5-50 nucleotides;

Y1+Z1=20 to 40 nucleotides;

wherein Y1 comprises 5-20 nucleotides 3′ to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR;

wherein Z1 comprises 5-20 nucleotides in the 5′ to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR; and

wherein W is a nucleotide complementary to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In some embodiments, the collection of probes specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, further comprises:

(n) Y1-X2-Z1-V

where X2 is from 10-50 nucleotides; and

wherein V is a nucleotide complementary to a wildtype sequence at the site of a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In specific embodiments, the collection of probes specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, further comprises:

(n) Y1-X2-Z1-V

where X2 is from 10-50 nucleotides and differs from X1; and

wherein V is a nucleotide complementary to a wildtype sequence at the site of a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In some embodiments, X1 is from 25-50 nucleotides. In certain embodiments, X1 comprises at least one labeled nucleotide. In some embodiments, each probe (a)-(g) has the same X1. In some embodiments, each probe selected from (a)-(g), (k) and (m) has the same X2.

In certain aspects, each of Y1+Z1, Y2+Z2 and Y3+Z3 is at least 25 nucleotides.

In certain aspects, each probe in the collection of probes has a GC content of at least 40%.

Some embodiments provide a collection of padlock probes specific for mutations to the KRAS gene, specific for mutations to the Braf gene, specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, and optionally collections of padlock probes specific for corresponding wild-type sequences, e.g. as defined above, the collection being capable of detecting a plurality of mutations in (i) the KRAS gene, (ii) the KRAS gene and the Braf gene, (iii) the KRAS gene and the APC gene, (iv) the KRAS gene and the PTEN gene, or (v) the KRAS gene and the PI3K gene, wherein the plurality of mutations constitute at least 40% of KRAS mutations associated with cancer.

Additional embodiments provide a collection of padlock probes specific for mutations to the KRAS gene, specific for mutations to the Braf gene, specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, and optionally collections of padlock probes specific for corresponding wild-type sequences, e.g. as defined above, wherein the detection of mutations to (i) the KRAS gene, (ii) the KRAS gene and the Braf gene, (iii) the KRAS gene and the APC gene, (iv) the KRAS gene and the PTEN gene, or (v) the KRAS gene and the PI3K gene allows to determine the presence of cancer or a predisposition for cancer.

In a specific embodiment the cancer or predisposition for cancer is determined in at least or in at most 5%, 10%, 15%, 20%, 25%, 30%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95% (or any range derivable therein) of patients bearing a KRAS-mutant associated with tumor development.

Further embodiments provide the use of a collection of padlock probes specific for mutations to the KRAS gene, specific for mutations to the Braf gene, specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, and optionally collections of padlock probes specific for corresponding wild-type sequences, e.g. as defined above, for the determination of the presence or absence of a KRAS-mutant tumor or for the determination of a predisposition for a KRAS-mutant tumor in a patient or group of patients.

In specific embodiments, the determination of the presence or absence of a KRAS-mutant tumor or for the determination of a predisposition for a KRAS-mutant tumor in a patient or group of patients allows to determine the presence of cancer in at least or in at most 5%, 10%, 15%, 20%, 25%, 30%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95% (or any range derivable therein) of a patient group bearing a KRAS-mutant associated with tumor development.

A “patient bearing a KRAS-mutant associated with tumor development” or a “patient group bearing a KRAS-mutant associated with tumor development” refers to an individual or group of individuals, wherein each patient or group member comprises at least one mutation in the KRAS gene (or a corresponding mutant), that has been described in the scientific literature or is known to the skilled person as being associated with tumor development, e.g., associated with preforms of tumors or predispositions for tumors, associated with different tumor development stages, or associated with full grown tumors or cancer. In specific embodiments, these mutations or mutants comprise mutations as can be derived from the Sanger database as of Aug. 22, 2012 being associated with cancer or precancer (on the world wide web at sanger.ac.uk).

In specific embodiments, the patient group, i.e. each member of the patient group, may bear a KRAS-mutant associated with tumor development and an additional mutation in the Braf gene, and/or the APC gene, and/or PTEN gene, and/or the PI3K gene. These combinations of mutations may contribute to tumor development associated with KRAS mutations; or they may constitute mutational combinations associated with cancer or precancer forms, or predispositions for cancer. In further specific embodiments, the patient group, i.e., each member of the patient group, may bear a mutation in the Braf gene, and/or the APC gene, and/or PTEN gene, and/or the PI3K gene. These mutations are associated with cancer or precancer, or predispositions for cancer as can be derived from the Sanger database (on the world wide web at sanger.ac.uk). In further specific embodiments, the patient group, i.e. each member of the patient group, may bear a mutation in the EGFR gene, and/or the KRAS gene, and/or the Braf gene, and/or the APC gene, and/or PTEN gene, and/or the PI3K gene. These mutations are associated with cancer or precancer, or predisposition for cancer, as can be derived from the Sanger database (on the world wide web at sanger.ac.uk). Furthermore, examples of EGFR mutations that may be detected according to various embodiments, or that may be employed in the context of compositions described herein are shown in Table 7.

Methods also concern detecting or localizing a RNA transcript encoded by a gene listed in Table B. In certain embodiments, a padlock probe has a sequence that is identical or complementary to a mutation in the gene associated with cancer (which means the mutation has been correlated in a statistically significant way with the presence of cancer, pre-cancer, and/or risk of cancer). The mutation may or may not cause cancer. This padlock probe can be used, in some embodiments, in conjunction with a padlock probe that is identical or complementary to the wild-type version of the gene in order to detect a cancer mutation in the gene using methods described herein. In some embodiments, the mutation is a point mutation, frame shift, substitution, deletion, insertion, translocation, inversion, amplification, indel, or a combination thereof. The mutation may constitute a mutation of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleotides.

In certain embodiments, the cancer is colorectal cancer, lung cancer, pancreas cancer, prostate cancer, skin cancer, thyroid cancer, liver cancer, ovary cancer, endometrium cancer, kidney cancer, cancer of the brain, testis cancer, acute non lymphocytic leukemia, myelodysplasia, urinary bladder cancer, head and neck cancer or breast cancer. In further embodiments, the predispositions to cancer are predispositions to colorectal cancer, lung cancer, pancreas cancer, prostate cancer, skin cancer, thyroid cancer, liver cancer, ovary cancer, endometrium cancer, kidney cancer, cancer of the brain, testis cancer, acute non lymphocytic leukemia, myelodysplasia, urinary bladder cancer, head and neck cancer or breast cancer.

In further embodiments the colorectal cancer is metastatic colorectal cancer, adenocarcinoma, leiomyosarcoma, colorectal lymphoma, melanoma or neuroendocrine tumor. In other embodiments, the lung cancer is a non-small cell lung cancer (NSCLC), or small cell lung cancer (SCLC).

Also provided are collections of padlock probes specific for mutations to the KRAS gene, specific for mutations to the Braf gene, specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, and optionally collections of padlock probes specific for corresponding wild-type sequences, e.g. as defined above, or uses thereof, e.g. as defined above, allowing to determine

(i) the presence of colorectal cancer in at least 25 to 60% of a patient group bearing a KRAS-mutant associated with tumor development;

(ii) the presence of lung cancer in at least 25 to 60% of a patient group bearing a KRAS-mutant associated with tumor development;

(iii) the presence of pancreas cancer in at least 80 to 90% of a patient group bearing a KRAS-mutant associated with tumor development;

(iv) the presence of prostate cancer in at least 5 to 25% of a patient group bearing a KRAS-mutant associated with tumor development;

(v) the presence of skin cancer in at least 5 to 25% of a patient group bearing a KRAS-mutant associated with tumor development;

(vi) the presence of thyroid cancer in at least 5 to 60% of a patient group bearing a KRAS-mutant associated with tumor development;

(vii) the presence of liver cancer in at least 10 to 25% of a patient group bearing a KRAS-mutant associated with tumor development;

(viii) the presence of ovary cancer in at least 5 to 50% of a patient group bearing a KRAS-mutant associated with tumor development;

(ix) the presence of endometrium cancer in at least 10 to 40% of a patient group bearing a KRAS-mutant associated with tumor development;

(x) the presence of kidney cancer in at least 5 to 50% of a patient group bearing a KRAS-mutant associated with tumor development;

(xi) the presence of cancer of the brain in at least 5 to 15% of a patient group bearing a KRAS-mutant associated with tumor development;

(xii) the presence of testis cancer in at least 10 to 45% of a patient group bearing a KRAS-mutant associated with tumor development;

(xiii) the presence of acute non lymphocytic leukemia in at least 5 to 15% of a patient group bearing a KRAS-mutant associated with tumor development;

(xiv) the presence of urinary bladder cancer in at least 5% of a patient group bearing a KRAS-mutant associated with tumor development;

(xv) the presence of head and neck cancer in at least 5 to 10% of a patient group bearing a KRAS-mutant associated with tumor development; or

(xvi) the presence of breast cancer in at least 5 to 10% of a patient group bearing a KRAS-mutant associated with tumor development.

In some embodiments, the above-mentioned collections of probes are provided in a kit along with one or more of the following:

(ii) an reverse transcriptase primer comprising one or more locked nucleic acid and capable of hybridizing to the target RNA;

(iii) a reverse transcriptase;

(iv) a ribonuclease;

(v) a ligase;

(vi) a polymerase having 3′ exonuclease activity;

(vii) a detection probe capable of hybridizing to a complement of the padlock probe; or

(ix) nucleotides.

In further embodiments, methods are provided for localized in situ detection of mRNA which codes for one or more mutations of the KRAS gene in a sample of cells on a slide surface, comprising:

(a) generating cDNA from mRNA in the sample, wherein the primer is provided with a functional moiety capable of binding to or reacting with a cell or cellular component or an affinity binding group capable of binding to a cell or cellular component;

(b) adding a ribonuclease to the sample to digest the mRNA hybridized to the cDNA;

(c) contacting the sample with one or more padlock probes specific for mutations to the KRAS gene, wherein each padlock probe comprises a sequence selected from the collection of padlock probes specific for mutations to the KRAS gene, specific for mutations to the Braf gene, specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, and optionally collections of padlock probes specific for corresponding wild-type sequences, e.g. as defined above.

In one embodiment, there are methods for localized in situ detection of mRNA which codes for one or more mutations of the KRAS gene in a sample of cells on a slide surface, comprising: (a) generating cDNA from mRNA in the sample, wherein the primer is provided with a functional moiety capable of binding to or reacting with a cell or cellular component or an affinity binding group capable of binding to a cell or cellular component; (b) adding a ribonuclease to the sample to digest the mRNA hybridized to the cDNA; (c) contacting the sample with one or more padlock probes specific for mutations to the KRAS gene, wherein each padlock probe comprises a sequence selected from the group consisting of:

(a) Y1-X1-Z1-A

(b) Y1-X1-Z1-T

(c) Y1-X1-Z1-C

(d) Y2-X1-Z2-A

(e) Y2-X1-Z2-T

(f) Y2-X1-Z2-C, and

(g) Y3-X1-Z3-A;

where:

X1 is from 5-50 nucleotides;

Y1+Z1=20 to 40 nucleotides;

Y2+Z2=20 to 40 nucleotides;

Y3+Z3=20 to 40 nucleotides;

Y1 is GTGGCGTAGGCAAGA (SEQ ID NO:1), GTGGCGTAGGCAAG (SEQ ID NO:2), GTGGCGTAGGCAA (SEQ ID NO:3), GTGGCGTAGGCA (SEQ ID NO:4), GTGGCGTAGGC (SEQ ID NO:5), GTGGCGTAGG (SEQ ID NO:6), GTGGCGTAG, GTGGCGTA, GTGGCGT, GTGGCG, GTGGC, GTGG, GTG, GT, G;

Y2 is TGGCGTAGGCAAGAG (SEQ ID NO:7), TGGCGTAGGCAAGA (SEQ ID NO:8), TGGCGTAGGCAAG (SEQ ID NO:9), TGGCGTAGGCAA (SEQ ID NO:10), TGGCGTAGGCA (SEQ ID NO:11), TGGCGTAGGC (SEQ ID NO:12), TGGCGTAGG, TGGCGTAG, TGGCGTA, TGGCGT, TGGCG, TGGC, TGG, TG, T;

Y3 is TGGCGTAGGCAAGAGTGC (SEQ ID NO:13), TGGCGTAGGCAAGAGTG (SEQ ID NO:14), TGGCGTAGGCAAGAGT (SEQ ID NO:15), TGGCGTAGGCAAGAG (SEQ ID NO:7), TGGCGTAGGCAAGA (SEQ ID NO:8), TGGCGTAGGCAAG (SEQ ID NO:9), TGGCGTAGGCAA (SEQ ID NO:10), TGGCGTAGGCA (SEQ ID NO:11), TGGCGTAGGC (SEQ ID NO:12), TGGCGTAGG, TGGCGTAG, TGGCGTA, TGGCGT, TGGCG, TGGC, TGG, TG, T; Z1 is TGGTAGTTGGAGCT (SEQ ID NO:27), GGTAGTTGGAGCT (SEQ ID NO:28), GTAGTTGGAGCT (SEQ ID NO:29), TAGTTGGAGCT (SEQ ID NO:30), AGTTGGAGCT (SEQ ID NO:31), GTTGGAGCT, TTGGAGCT, TGGAGCT, GGAGCT, GAGCT, AGCT, GCT, CT, T, or a bond; Z2 is GGTAGTTGGAGCTG (SEQ ID NO:16), GTAGTTGGAGCTG (SEQ ID NO:17), TAGTTGGAGCTG (SEQ ID NO:18), AGTTGGAGCTG (SEQ ID NO:19), GTTGGAGCTG (SEQ ID NO:20), TTGGAGCTG, TGGAGCTG, GGAGCTG, GAGCTG, AGCTG, GCTG, CTG, TG, G or a bond; and Z3 is AGTTGGAGCTGGTG (SEQ ID NO:21), GTTGGAGCTGGTG (SEQ ID NO:22), TTGGAGCTGGTG (SEQ ID NO:23), TGGAGCTGGTG (SEQ ID NO:24), GGAGCTGGTG (SEQ ID NO:25), GAGCTGGTG (SEQ ID NO:26), AGCTGGTG, GCTGGTG, CTGGTG, TGGTG, GGTG, GGTG, GTG, TG, G or a bond; (d) ligating, directly or indirectly, the ends of the padlock probe(s); (e) subjecting the circularized padlock probe(s) to rolling circle amplification (RCA) using a DNA polymerase having 3′-5′ exonuclease activity wherein if necessary the exonuclease activity digests the cDNA to generate a free 3′ end which acts as a primer for the RCA; and (f) detecting the rolling circle amplification product(s).

In some embodiments of the method, step (c) further comprises contacting the sample with padlock probes (h), (i) and (j), wherein each is specific for wild-type KRAS gene and have sequences:

(h) Y1-X2-Z1-G

(i) Y2-X2-Z2-G, and

(j) Y3-X2-Z3-G

where X2 is from 10-50 nucleotides.

In specific embodiments of the method, step (c) further comprises contacting the sample with padlock probes (h), (i) and (j), wherein each is specific for wild-type KRAS gene and have sequences:

(h) Y1-X2-Z1-G

(i) Y2-X2-Z2-G, and

(j) Y3-X2-Z3-G

where X2 is from 10-50 nucleotides and differs from X1.

In a further embodiment, there are methods for localized in situ detection of mRNA which codes for one or more mutations of the Braf gene in a sample of cells on a slide surface, comprising:

(a) generating cDNA from mRNA in the sample, wherein the primer is provided with a functional moiety capable of binding to or reacting with a cell or cellular component or an affinity binding group capable of binding to a cell or cellular component;

(b) adding a ribonuclease to the sample to digest the mRNA hybridized to the cDNA;

(c) contacting the sample with one or more padlock probes specific for mutations to the Braf gene, wherein each padlock probe comprises a sequence selected from the group consisting of:

(k) Y1-X1-Z1-A

where:

X1 is from 5-50 nucleotides;

Y1+Z1=20 to 40 nucleotides;

Y1 is GAAATCTCGATGGAG (SEQ ID NO:102), AAATCTCGATGGAG (SEQ ID NO:103), AATCTCGATGGAG (SEQ ID NO:104), ATCTCGATGGAG (SEQ ID NO:105), TCTCGATGGAG (SEQ ID NO:106), CTCGATGGAG (SEQ ID NO:107), TCGATGGAG, CGATGGAG, GATGGAG, ATGGAG, TGGAG, GGAG, GAG, AG, G; and

Z1 is TGGTCTAGCTACAG (SEQ ID NO:108), GGTCTAGCTACAG (SEQ ID NO:109), GTCTAGCTACAG (SEQ ID NO:110), TCTAGCTACAG (SEQ ID NO:111), CTAGCTACAG (SEQ ID NO:112), TAGCTACAG, AGCTACAG, GCTACAG, CTACAG, TACAG, ACAG, CAG, AG, G, or a bond;

(d) ligating, directly or indirectly, the ends of the padlock probe(s);

(e) subjecting the circularized padlock probe(s) to rolling circle amplification (RCA) using a DNA polymerase having 3′-5′ exonuclease activity wherein if necessary the exonuclease activity digests the cDNA to generate a free 3′ end which acts as a primer for the RCA; and (f) detecting the rolling circle amplification product(s).

In some embodiments of the method, step (c) further comprises contacting the sample with padlock probes (l), wherein each is specific for wild-type Braf gene and have sequences:

(l) Y1-X2-Z1-T

where X2 is from 10-50 nucleotides.

In specific embodiments of the method, step (c) further comprises contacting the sample with padlock probes (l), wherein each is specific for wild-type Braf gene and have sequences:

(l) Y1-X2-Z1-T

where X2 is from 10-50 nucleotides and differs from X1.

In a further embodiment, methods are provided for localized in situ detection of mRNA which codes for one or more mutations of the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR in a sample of cells on a slide surface, comprising:

(a) generating cDNA from mRNA in the sample, wherein the primer is provided with a functional moiety capable of binding to or reacting with a cell or cellular component or an affinity binding group capable of binding to a cell or cellular component;

(b) adding a ribonuclease to the sample to digest the mRNA hybridized to the cDNA;

(c) contacting the sample with one or more padlock probes specific for mutations to the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR, wherein each padlock probe comprises a sequence selected from the group consisting of: (m) Y1-X1-Z1-W where: X1 is from 5-50 nucleotides; Y1+Z1=20 to 40 nucleotides; wherein Y1 comprises 5-20 nucleotides 3′ to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR; wherein Z1 comprises 5-20 nucleotides in the 5′ to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR; and wherein W is a nucleotide complementary to a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In some embodiments of the method step (c) further comprises contacting the sample with padlock probes (n), wherein each is specific for wild-type APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR and have sequences:

(n) Y1-X2-Z1-V

where X2 is from 10-50 nucleotides; and

wherein V is a nucleotide complementary to a wildtype sequence at the site of a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In specific embodiments of the method step (c) further comprises contacting the sample with padlock probes (n), wherein each is specific for wild-type APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR and have sequences:

(n) Y1-X2-Z1-V

where X2 is from 10-50 nucleotides and differs from X1; and

wherein V is a nucleotide complementary to a wildtype sequence at the site of a point mutation in the APC gene, PTEN gene, PI3K gene, KRAS gene codon 61 or codon 146, or KRAS gene 3′UTR.

In some embodiments, X1 and X2 each comprise at least one labeled nucleotide. In certain aspects, the label is fluorophore or a chromophore. In certain embodiments, each probe selected from (a)-(g), (k) and (m) has the same X1. In certain embodiments, each probe selected from (h)-(j), (l) and (n) has the same X2.

In certain embodiments of the method, the primer comprises 2′O-Me RNA, methylphosphonates or 2′ Fluor RNA bases, peptidyl nucleic acid residues, or locked nucleic acid residues. In additional embodiments, a primer is modified with biotin, an amine group, a lower alkylamine group, an acetyl group, DMTO, fluoroscein, a thiol group, or acridine. In some embodiments, the sample comprises a fixed tissue section, a fresh frozen tissue, touch imprint samples or a cytological preparation comprising one or more cells.

It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein.

The terms “comprise” (and any form of comprise, such as “comprises” and “comprising”), “have” (and any form of have, such as “has” and “having”), “contain” (and any form of contain, such as “contains” and “containing”), and “include” (and any form of include, such as “includes” and “including”) are open-ended linking verbs. As a result, a method, composition, kit, or system that “comprises,” “has,” “contains,” or “includes” one or more recited steps or elements possesses those recited steps or elements, but is not limited to possessing only those steps or elements; it may possess (i.e., cover) elements or steps that are not recited. Likewise, an element of a method, composition, kit, or system that “comprises,” “has,” “contains,” or “includes” one or more recited features possesses those features, but is not limited to possessing only those features; it may possess features that are not recited.

Any embodiment of any of the present methods, composition, kit, and systems may consist of or consist essentially of—rather than comprise/include/contain/have—the described steps and/or features. Thus, in any of the claims, the term “consisting of” or “consisting essentially of” may be substituted for any of the open-ended linking verbs recited above, in order to change the scope of a given claim from what it would otherwise be using the open-ended linking verb.

The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.”

Throughout this application, the term “about” is used to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value.

Following long-standing patent law, the words “a” and “an,” when used in conjunction with the word “comprising” in the claims or specification, denotes one or more, unless specifically noted.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1: Schematic representation of the detection of individual transcripts in situ with padlock probes and target-primed RCA. cDNA is created using locked nucleic acid (LNA)-modified primers and is probed after degradation of mRNA by RNase H. RCPs are identified through hybridization of fluorescent detection probes.

FIG. 2: Multiplex in situ detection of cancer-related transcripts in cancer and primary human cell lines. Quantification of RCPs in the different cell lines is shown in the bar graph: (a) human ovarian carcinoma cells (SKOV3); (b) human breast carcinoma cells (SKBR3); (c) TERT immortalized human fibroblast cells (BJhTERT); and (d) primary human fibroblast culture GM08402.

FIG. 3: Effect of LNA base incorporation in the primer for cDNA synthesis in situ. cDNA primers with different LNA substitutions were compared against an unmodified primer consisting of only DNA bases (No mod) for cDNA synthesis in situ. Synthesized cDNA was detected with padlock probes and target-primed RCA and quantified by counting RCPs/cell. The investigated primers had five, seven or nine LNA bases positioned either at every second or every third position in the 5′-end of the primers. Primers had a total length of 25 nt or 30 nt (indicated in parentheses).

FIG. 4: Investigation of cDNA synthesis length. Primers positioned at different distances from the mRNA 5′-end, where the target site of the PLP-βe1 padlock probe is located, were compared for in situ detection of β-actin transcripts with padlock probes and target-primed RCA to investigate the efficiency of the cDNA synthesis. When reverse transcription was carried out without addition of any primer, an average of seven RCPs were detected per cell (not shown in diagram).

FIG. 5: Detection of individual β-actin transcripts in cultured human fibroblasts. Target sites in exons 1 and 6 on the β-actin transcript were probed in GM08402 cells. A negative control was performed without addition of reverse transcriptase.

FIG. 6: Quantification of RCPs in single cultured cells. Histogram showing quantification of (a) β-actin RCPs in 134 cells of a GM08402 culture and (b) KRAS RCPs in 77 cells of an A-427 culture.

FIG. 7: In situ genotyping of KRAS codon 12 mutations in cell lines with padlock probes and RCA. Quantification of the number of RCPs/cell detected in situ in the heterozygous cell line A-427, showing the allelic expression of wild type (light grey) and mutated (dark grey) KRAS-RCPs in single cells. Inset represents the overall allelic ratio from 77 counted cells.

FIG. 8: Schematic overview for in situ genotyping with padlock probes and target-primed RCA. KRAS cDNA (black) is created by reverse transcription with an LNA-primer. Target mRNA (grey) is degraded by RNase H, except for the region that is hybridized to the LNA-part of the primer that is protected from degradation, anchoring the created cDNA to the target. KRAS genotype specific padlock probes, with similar target sites except for the single point mutated base (GGT→AGT), are hybridized to the cDNA and circularized by target-dependent ligation. The targeted KRAS transcripts act as primer for RCA and the resulting RCPs are labeled with fluorescence-labeled detection probes and visualized as bright spots in the cells or tissue.

FIG. 9: Example of padlock probes for a Braf mutant and wild-type sequence.

DETAILED DESCRIPTION OF THE INVENTION A. Localized Synthesis of cDNA from RNA Targets In Situ

As discussed above, some embodiments concern the detection of RNA, especially mRNA, in cells. The method involves the conversion of RNA to complementary DNA (cDNA) prior to the targeting of the cDNA with a padlock probe(s). The cDNA is synthesized in situ at the location of the template RNA. The reverse transcriptase (RT) primer may be modified so as to be capable of immobilization, and in particular immobilization to the cell. Thus it is contemplated that the primer may be provided with a functional moiety, or functional means (i.e. a “functionality”), which allows or enables the primer to be immobilized to a component in the sample, e.g. a cell or cellular component. This may be for example a functional moiety capable of binding to or reacting with a cell or a sample or cellular component. The use of such a primer, which becomes immobilized to the sample (e.g. to or in a cell), has the result that the cDNA product (which is generated by extension of the RT primer and is therefore contiguous with it) also becomes immobilized to the sample (e.g. to or in a cell). Methods and compositions are discussed in Application PCT/IB2012/000995, U.S. patent application Ser. No. 13/397,503, U.S. Provisional Application Ser. No. 61/473,662, and U.S. Provisional Application Ser. No. 61/442,921, which are hereby incorporated by reference.

Since the RCA, which is performed to generate the RCP that is ultimately detected, is carried out using the cDNA as primer (i.e. is a target-primed RCA) the RCP is contiguous with the cDNA and thus the RCP is also anchored or attached to the sample (e.g. cell). Thus, the use of such a primer ensures or allows that the RCP remains localized to the site of the RNA in the sample (e.g. in the cell). In other words localization of the RCP to the original site of the target RNA is preserved. In this way, localization of the signal reporting the target RNA is preserved and thus it can be seen that this favors and facilitates localized in situ detection.

Various such modifications of the RT primer are described herein and include, for example, the provision of reactive groups or moieties in the RT primer, e.g. chemical coupling agents such as a thiol group, NHS-esters, etc., which are capable of covalent attachment to the cells or cellular or other sample components, e.g. to proteins or other biomolecules in the cell, or to components in the sample e.g. matrix components in the sample. Alternatively or in addition, the primer may be provided with an affinity binding group capable of binding to a cell or cellular or sample component.

In particular embodiments, a nucleic acid molecule, such as a primer or probe, has been modified to alter its characteristics, such as functionality or activity. In some embodiments, the nucleic acid is subject to depurination and ketone functionalization. Depurination of DNA introduces an aldehyde group which undergoes the full range of reactions expected of aldehydes including the Cannizaro reaction, Cyanohydrin formation, hydration, hydrazine derivatisation, hydrolysis, reductive amination reaction, Schiff base formation, Wolff-Kishner reduction, and reactions with Grignard reagents. The example is further exemplified by the reactions of a hydrazone followed by sodium cyanoborohydride reduction. See Mirzabekov, A.; Proudnikov, D. Nucleic Acid Research 1996, 24, 4535; McMurry, J. Organic Chemistry 4^(th) Ed, Brooks/Cole 1995; Hermann, G. T. Bioconjugate Techniques 2^(nd) Ed, Elsevier, 2008; US2009011836; Dey, S.; Sheppard, T. L. Organic Letters. 2001, 3, 3983, all of which are hereby incorporated by reference in their entirety.

In other embodiments, a nucleic acid molecule such as a probe or primer has substituted purines, which can then be crosslinked. Heterocyclic bases, nucleotides, nucleotide analogues and alkylating agents which when incorporated into the backbone of the sequence can be covalently cross-linked, such as described in U.S. Pat. No. 6,232,463, which is hereby incorporated by reference. Other examples involve labeled nucleic acids. Included are a variety of methods to form linkers with azide functionalised nucleic acids, these include the Wittig-Horner reaction, imine formation, ether formation, for example by the Williamson method or by the palladium-catalysed Buchwald method, Claisen ester condensation, Ziegler nitrile condensation, acyloin condensation, Ruzicka condensation of carboxylic acid salts of cerium or of thorium, ester formation, amide formation, 4+2 cycloaddition, for example Diels-Alder reaction, Buchwald amination, Suzuki coupling or olefin metathesis. See, for instance, U.S. Pat. No. 8,114,636, which is hereby incorporated by reference.

Other alterations may be implemented using click chemistry, which has been utilized to covalently link DNA and fluorophores through Cu^(I) [3+2] azide-alkyne cycloaddition (CuAAC) reaction and 1,3-dipolar cycloaddition chemistry (Husigens AAC reaction). Brown, T.; El-Sagheer, A. H. Chem. Soc. Rev., 2010, 39, 1388 and U.S. Patent Publication 2008/0311412, both of which are hereby incorporated by reference. Another modification that may be employed with nucleic acids used in methods described herein include thiol modifications and amini modifications. DNA can be commercially bought with a thiol modification that allows the DNA crosslinking through a range of standard thiol chemistry including the formation of dithiols, reactions with maleimides, Haloacetyls, pyridyl disulphides, acrydites, and acryloyls (Hermann, G. T. Bioconjugate Techniques 2^(nd) Ed, Elsevier, 2008, which is hereby incorporated by reference). Amine modification DNA can be crosslinked through a range of standard amine chemistry including the formation of isothiocyanates, acyl azides, NHS esters, sulfonyl chlorides, aldehydes, glyoxals, epoxides, oxiranes, carbonates, arylating agents, carbodiimides, and anhydrides (Hermann, G. T. Bioconjugate Techniques 2^(nd) Ed, Elsevier, 2008, which is hereby incorporated by reference). As discussed in detail elsewhere, there are several sites on a nucleic acid at which covalent attachment is possible; these include the sugar, the phosphate, the purine and pyrimidine bases (Kricka, L, J. Clinical Chemistry, 2009, 55, 670, which is hereby incorporated by reference).

In some embodiments, enzymatic modification of a nucleic acid strand may be employed. Oligonucleotide sequences can be modified through the enzymatic action to increases reactivity. For example in the presence of adenosine triphosphate the 5′ end of a single strand sequence is adenylated allowing for further crosslinking with hydroxyls (U.S. Pat. No. 4,464,359, which is hereby incorporated by reference). Another technique that can be used is functional biopolymer modification and reagents. Bifunctional phosphorus containing monomers can be incorporated into the oligonucleotide sequence during synthesis, this allows for the introduction of phosphorus based coupling groups including phosphoramidites, phosphonamidites, H-phosphonates, phosphodiesters, phosphotriesters, thiophosphoramidates, thionoalkylphosphonates, thionoalkyl-phosphotriesters and boranophosphates. These reagents also posses a protected hydrazino or oxyamino group including heteroaromatic hydrazine, semicarbazide, carbazide, thiosemicarbazide, thiocarbazide, carbonic acid dihydrazine or hydrazine carboxylate which undergo coupling reactions (U.S. Pat. No. 7,732,628 and U.S. Patent Publication 20110319606, which are both hereby incorporated by reference). The use of psoralens is another modification that may be employed. Psoralens (furocumarins) intercalating between bases and forming permanently bonded adducts between mRNA and primer sequences upon exposure to UV (Lipson, E. S.; Hearst, J. E. Methods in Enzomology, 1998, 164, 330 and U.S. Pat. No. 4,124,598, which are hereby incorporated by reference).

For sequencing applications, the terminal phosphate group is used as a linker to EDC activated surfaces (U.S. Patent Publication 20100167299, which is hereby incorporated by reference). Accordingly, nucleic acid molecules have a phospholink nucleotide(s) in some embodiments.

Although cells or cellular components provide a convenient point of attachment, or site of immobilization of the RT primer, this aspect is not restricted to immobilization on or within cells, and the RT primer may be immobilized to other components present in the sample, for example extracellular components. Indeed the components may be natural or synthetic and synthetic components may be added to the sample to supplement or to replace native cellular components. For example, a synthetic matrix may be provided to a cell or tissue sample to preserve signal localization in the method (namely to preserve localization of the RCP product which is detected). Indeed, rather than immobilizing the RT primer (as a means of immobilizing the cDNA), the synthesized cDNA itself or the target RNA may be immobilized in a synthetic matrix which is provided to the sample.

Thus for example, the target RNA or the synthesized cDNA may be attached to a synthetic gel matrix instead of the native cellular matrix to preserve the localization of the detection signals. This may be achieved by immersing the sample (e.g. the cells or tissue of the sample) in a gel solution which upon polymerization will give rise to a gel matrix to which the cDNA or target RNA can be attached. To achieve such attachment the RT primer may be provided with a reactive group or moiety which can react with the matrix material, for example at the 5′ end thereof. This is described further below.

In one embodiment, modification, however, the primer is rendered resistant to the ribonuclease. Thus the primer may be modified to be ribonuclease-resistant. A ribonuclease is utilized to digest the RNA hybridized to the cDNA in an RNA:DNA duplex. As discussed below, in some embodiments a ribonuclease made be added or a sample may be incubated under conditions that allow a ribnuclease to digest RNA. In some cases, an endogenous ribonuclease may be employed. In certain embodiments, the ribonuclease may be RNase H or a ribonuclease capable of digesting RNA in an RNA:DNA duplex. In some embodiments, immobilization of the reverse transcriptase primer is achieved by virtue of it being ribonuclease resistant. In such a situation the ribonuclease cannot degrade the RNA which is hybridized to the RT primer. Thus the RT primer protects the primer binding site in the RNA from degradation. The RT primer accordingly remains bound to the RNA in the cell and in this way is immobilized in the cell. Modifications which may be made to the primer to render it ribonuclease-resistant are described below and include in particular the use of modified nucleotides, or nucleotide analogues for example nucleotides comprising 2′O-Me RNA, methylphosphonates, 2′ fluor RNA bases, etc. which when incorporated into the primer, render the primer at least partially resistant to ribonuclease digestion. Alternatively or in addition, the primer may comprise locked nucleic acids (LNAs) or peptide nucleic acids (PNAs). Thus, in some embodiments, it is envisaged that the 5′ end of the cDNA remains bound to the target RNA molecule via a ribonuclease resistant reverse transcriptase primer.

Methods may involve digestion of mRNA, but in some embodiments, complete digestion of mRNA is not desirable because this allows the primer and hybridized cDNA to diffuse within the cell, which may reduce specificity and resolution. Therefore, in certain embodiments, methods are employed to reduce this by chemically modifying the mRNA and/or the primers to enhance RNase resistance. In other embodiments, a primer is modified to promote its surface conjugation to native proteins in order to prevent its diffusion.

Embodiments for chemical modification of mRNA and primers to inhibit RNase digestion include a variety of techniques. SHAPE is Selective 2′-Hydroxyl Acylation Analyse by Primer Extension. It involves a 2′-OH group present in a nucleotide backbone that is an essential component in the mechanism of mRNA hydrolysis by RNase. It has been demonstrated that nucleotide backbone exposure to electrophilic reagents results in 2-O′ adducts that inhibit RNase digestion, providing chemical resistance. Reagents include 1-methyl-7-nitroisatoic (1M7) and N-methylisatoic anhydride (NMIA). Therefore sight selective synthesis at the appropriate position on the backbone should provide RNAse resistance to both a primer and mRNA. See Steen, et al., Nature Protocols 2011, 6, 1683, Merino, et al., J. Am. Chem. Soc. 2005, 127, 4223, which are both hereby incorporated by reference. Another protocol involves modification of the phosphate backbone. Part of the RNase digestion mechanism involves cyclization of the phosphodiester nucleotide backbone bond with 2′-OH. Modification of this group through the synthesis of phosphorothioates, N3′-P5′ phosphoamidates and all of their derivatives prevents RNase hydrolysis by preventing the traditional mechanistic route, and therefore providing site selective RNase resistance. See Gao, et al., Mol Pharmacol, 1992, 41, 223, U.S. Pat. No. 6,143,881, Gryaznoz; J. Am. Chem. Soc. 1994, 116, 3143, and U.S. Pat. No. 4,415,732, all of which are incorporated by reference. The use of metal chelators may also be implemented. It has been demonstrated that transition metals such as vanadium (v), oxocanadium (IV) and oxorhenium (V) form metal chelates with the Uracil backbone of RNA. This complex prevented RNase digesting beyond this point therefore site selective chelation may therefore provide a further method for RNase resistance. See Janda, et al. Am. Chem. Soc. 1996, 118, 12521, and U.S. Pat. No. 4,837,312, which are hereby incorporated by reference. Another technique involves primer-mRNA crosslinking. Chemically crosslinking the primer to mRNA will ensure that the primer will neither dissociate from the point of conjugation and also ensure that RNase can not hydrolyse the mRNA through adding steric hindrance. There are various methods of crosslinking including those involving: psoralens (furocumarins) intercalating between bases and forming permanently bonded adducts between mRNA and primer sequences upon exposure to UV; thiolation of bases to from dithiols; metal complexation; 1,4-phenyldiglyoxal crosslinking between sequences; quinine crosslinking between sequences; and, azinomycin crosslinking between sequences. See Lipson et al., Methods in Enzymology, 1998, 164, 330, Sigurdsson, S. J.; Methods, A Companion to Methods in Enzymology, 1999, 18, 71, Mohammed et al., Bio-Organic and Medicinal Chem. Let. 1999, 9, 1703, Wagner et al., Nucleic Acid Research, 1978, 5, 4065, Pang et al, J. Am. Chem. Soc. 2003, 125, 1116, Alcaro et al., J. Chem. Inf. Model. 2005, 45, 602, U.S. Pat. No. 5,681,941, and U.S. Pat. No. 4,196,281, all of which are hereby incorporated by reference.

In other embodiments, chemical modification of the primer may be implemented to allow for its suface conjuction with native proteins. A variety of techniques may be employed. For example, methods may involve chemical coupling of modified primers to proteins native to the sample surface. If complete digestion of mRNA occurs the primer-cDNA complex will dissociate from its point of origin, reducing resolution and sensitivity. To prevent this one may modify the primer backbone/5′ end so that it contains a chemical group that can bind with any native proteins on the sample surface. As there is little opportunity to modify the sample prior to use, the conjugation possibilities include four native groups (primary amine, carboxyls, thiols and carbonyls) on the protein surface. There are currently multiple cross-linkers that can be added to the primer to ensure conjugation including: amine reactive groups such as NHS esters, imidoesters and hydroxymethyl phosphene; carboxyl reactive groups such as carbodiimides' thiol reactive groups such as malemides, thiosulphonates and vinylsulphones; and, carbonyl reactive groups such as hydrazide. Functionalization of the primer with any of these groups followed by the appropriate conditions should cross link the primer to the surface following hybridisation to mRNA ensuring even if complete digestion occurs the primer/cDNA will not dissociate. See Hermann, G. T. Bioconjugate Techniques 2^(nd) Ed, Elsevier, 2008, which is hereby incorporated by reference.

In some embodiments, a nucleic acid such as a primer may be modified to provide one or more additional properties. In some embodiments, the modification enables the primer to be resistant to degradation, as discussed above. In other embodiments, the modification enables the primer to be attached or localized. In certain embodiments, the modification allows the primer to be crosslinked to one or more chemical moieties. In some cases, the crosslinking occurs via a linker that may or may not be cleavable. In some embodiments, there may be a primary amine reactive group, while in others, there may be a thiol reactive group. In further embodiments, both functional groups may be employed in a linker.

In another example, heterobifunctional cross-linking reagents and methods of using the cross-linking reagents are described (U.S. Pat. No. 5,889,155, specifically incorporated herein by reference in its entirety). The cross-linking reagents combine a nucleophilic hydrazide residue with an electrophilic maleimide residue, allowing coupling in one example, of aldehydes to free thiols. The cross-linking reagent can be modified to cross-link various functional groups and is thus useful for cross-linking polypeptides and sugars. Table A details certain hetero-bifunctional cross-linkers considered useful in the some embodiments. Moreover, the following references disclose information about such linkers, and are hereby incorporated by reference: Hermann, G. T. Bioconjugate Techniques 2^(nd) Ed, Elsevier, 2008; May, J. M, Biochemistry, 28, 1718; Fujiwara, K., J. Immunol. Methods. 1998, 112, 77; Tiberi, M., J. Biol. Chem. 1996, 271, 3771; Kitagawa, T. Chem. Pharm. Bull. 1981, 29, 1130; Trail, P, A. Science, 1993, 261, 212.

TABLE A HETERO-BIFUNCTIONAL CROSS-LINKERS Spacer Arm Length\after Linker Reactive Toward Advantages and Applications cross-linking SMPT Primary amines Greater stability 11.2 A Sulfhydryls Sulfo-LC-SMPT Primary amines to Water Soluble 20.0 A Sulfhydryls SPDP Primary amines Thiolation  6.8 A Sulfhydryls Cleavable cross-linking LC-SPDP Primary amines Extended spacer arm 15.6 A Sulfhydryls Sulfo-LC-SPDP Primary amines Extended spacer arm 15.6 A Sulfhydryls Water-soluble SMCC Primary amines Stable maleimide reactive group 11.6 A Sulfhydryls Enzyme-antibody conjugation Hapten-carrier protein conjugation Sulfo-SMCC Primary amines Stable maleimide reactive group 11.6 A Sulfhydryls Water-soluble Enzyme-antibody conjugation AMAS Primary amines Low potential for immune  4.4 A Sulfhydryls response BMPS Primary amines Low potential for immune Sulfhydryls response MBS Primary amines Enzyme-antibody conjugation  9.9 A Sulfhydryls Hapten-carrier protein conjugation Sulfo-MBS Primary amines Water-soluble  9.9 A Sulfhydryls GMBS Primary amines Increased stability over MBS 10.2 A Sulfhydryls Sulfo-GMBS Primary amines Water-soluble 10.2 A Sulfhydryls EMCS Primary amines Low potential for immune  9.4 A Sulfhydryls response Sulfo-EMCS Primary amines Water-soluble  9.4 A Sulfhydryls SIAB Primary amines Enzyme-antibody conjugation 10.6 A Sulfhydryls Sulfo-SIAB Primary amines Water-soluble 10.6 A Sulfhydryls SMPB Primary amines Extended spacer arm 14.5 A Sulfhydryls Enzyme-antibody conjugation Sulfo-SMPB Primary amines Extended spacer arm 14.5 A Sulfhydryls Water-soluble Sulfo-KMUS Primary amines Water-soluble 16.3 A Sulfhydryls SMPH Primary amines Non-cleavable 14.2 A Sulfhydryls SIAX/SIAXX Primary amines Highly specific to sulfhydryls 10.5 A/24 A Sulfhydryls Good membrane penetration SIAC/SIACX Primary amine Highly specific to sulfhydryls 12.0 A/24 A Sulfhydryls NPIA Primary amine Short linker allows for the study of  3.0 A Sulfhydryls biological interactions SATA Primary amine Hapten-carrier protein conjugation  6.5 A Sulfhydryls EDC/Sulfo-NHS Primary amines Hapten-Carrier conjugation  0 Carboxyl groups ABH Carbohydrates Reacts with sugar groups 11.9 A Nonselective NHS-ASA Primary amines Reacts with sugar groups  8.0 A Photoreactives Sulfo-NHS-ASA Primary amines Provides an iodination site for  8.0 A Photoreactives tracking Sulfo-NHS-LC- Primary amines Extended spacer arm 18.0 A ASA Photoreactives Water-soluble SASD Primary amines Water-soluble 18.9 A Photoreactives Potentially Cleavable HSAB Primary amines Short linker allows for stable  9.0 A Photoreactives derivatives NHS-ASA Primary amines Reacts with sugar groups  8.0 A Photoreactives Sulfo-NHS-ASA Primary amines Provides an iodination site for  8.0 A Photoreactives tracking Sulfo-NHS-LC- Primary amines Extended spacer arm 18.0 A ASA Photoreactives Water-soluble SASD Primary amines Water-soluble 18.9 A Photoreactives Potentially Cleavable HSAB Primary amines Short linker allows for stable  9.0 A Photoreactives derivatives Sulfo-HSAB Primary amines Water-soluble  9.0 A Photoreactives SANPAH Primary amines Selectivly activates reactive 18.2 A Photoreactives nitrenes Sulfo-SANPAH Primary amines Water-soluble 18.2 A Photoreactives SAND Primary amines Water-soluble 18.5 A Photoreactives Photoactive at higher wavelengths ANB-NOS Primary amines Photoactive at higher wavelengths  7.7 A Photoreactives SADP Primary amines Cleavable 13.9 A Photoreactives Sulfo-SADP Primary amines Water Soluble 13.9 A Photoreactives Sulfo-SAPB Primary amines Water Soluble 12.8 A Photoreactives SAED Primary amines Water Soluble 23.6 A Photoreactives Fluoresces after activation Sulfo-SAMCA Primary amines Fluoresces after activation 12.8 A Photoreactives PND Primary amines Potential bonding agent for 12.0 A Photoreactives paramagnetic beads PNP-DTP Primary amines Can probe active centres of 12.0 A Photoreactives receptor molecules Sulfo-SANPAH Primary amines Water Soluble 18.2 A Photoreactives Non cleavable NHS-Diazirine Primary amines Greater photostability than aryl  3.9 A Photoreactives azides Sulfo-NHS- Primary amines Greater photostability than aryl  3.9 A Diazirine Photoreactives azides SDA Primary amines Greater photostability than aryl  3.9 A Photoreactives azides Cleavable Sulfo-SDA Primary amines Greater photostability than aryl  3.9 A Photoreactives azides Cleavable Water Soluble Sulfo-LC-SDA Primary amines Greater photostability than aryl 12.5 A Photoreactives azides Cleavable Water Soluble Extended spacer arm BMPH Sulfhydryls Water Soluble  8.1A Carbohydrates Non Cleavable EMCH Sulfhydryls Non Cleavable 11.8 A Carbohydrates MPBH Sulfhydryls Extended spacer arm 17.9 A Carbohydrates KMUH Sulfhydryls Extended spacer arm 19.0 A Carbohydrates PDPH Sulfhydryls Cleavable  9.2 A Carbohydrates ASIB Sulfhydryls Excellent specificity 18.8 A Photoreactives APDP Sulfhydryls Extended spacer arm 19.5 A Photoreactives B4I Sulfhydryls High Yield 12.0 A Photoreactives ASBA Carboxylate Extended spacer arm 16.3 A Photoreactives

Examples of types of chemical reactions that might be employed include, but are not limited to the following: Diels-Alder chemistry, supramolecular chemistry, click chemistry, or thiol crosslinking (such as SMCC and other described below). Examples of modifications include biotin, amine molecules, thiol molecules, a combination of modifications discussed herein, dendrimers, and random primers.

Click chemistry that has been employed with nucleic acids is described in El-Sagheer et al., Chem. Soc. Rev. 2010, 39, 1388-1405, which is hereby incorporated by reference. This review describes the use of the copper catalyzed akyne-azide cycloaddition (CuAAC) reaction for use with nucleic acids. In particular embodiments, a primer may employ the CuAAC reaction to add a label to a nucleic acid, such as a fluorescent label, or to add a sugar, peptide, or other reporter groups.

A “reverse transcription reaction” is a reaction in which RNA is converted to cDNA using the enzyme “reverse transcriptase” (“RT”), which results in the production of a single-stranded cDNA molecule whose nucleotide sequence is complementary to that of the RNA template. However, reverse transcription results in a cDNA that includes thymine in all instances where uracil would have occurred in an RNA complement. The reverse transcription reaction is typically referred to as the “first strand reaction” as the single-stranded cDNA may subsequently be converted into a double-stranded DNA copy of the original RNA by the action of a DNA polymerase (i.e. the second strand reaction). However, in the present method, a single cDNA strand is formed to act as a target for a sequence-specific padlock probe. The reverse transcription reaction is catalyzed by an enzyme that functions as an RNA-dependent DNA polymerase. Such enzymes are commonly referred to as reverse transcriptases. Reverse transcriptase enzymes are well known in the art and widely available. Any appropriate reverse transcriptase may be used and the choice of an appropriate enzyme is well within the skill of a person skilled in the art.

B. Padlock Probes and RCA

As mentioned above, the cDNA serves as a target for a padlock probe. Embodiments relating to the use of padlock probes for detection of specific sequences can be found in U.S. Nonprovisional patent application Ser. No. 13/397,503, PCT Application PCT/US12/25279, U.S. Provisional Application Ser. No. 61/473,662, and U.S. Provisional Application Ser. No. 61/442,921, all of which are incorporated by reference in their entirety. Padlock probes are well known and widely used and are well-reported and described in the prior art. Thus the principles of padlock probing are well understood and the design and use of padlock probes is known and described in the art. Reference may be made for example to WO 99/49079. A padlock probe is essentially a linear circularizable oligonucleotide which has free 5′ and 3′ ends which are available for ligation, to result in the adoption of a circular conformation. It is understood that for circularization (ligation) to occur, the padlock probe has a free 5′ phosphate group. To allow the juxtaposition of the ends of the padlock probe for ligation, the padlock probe is designed to have at its 5′ and 3′ ends regions of complementarity to its target sequence (in this case the synthesized cDNA molecule in the cell sample to be analyzed). These regions of complementarity thus allow specific binding of the padlock probe to its target sequence by virtue of hybridization to specific sequences in the target. Padlock probes may thus be designed to bind specifically to desired or particular targets. In the case of some methods, the sequence of the cDNA target is defined by the sequence of the target RNA, i.e. the RNA molecule it is desired to detect. By hybridization to the cDNA target the ends of the padlock probe are brought into juxtaposition for ligation. As described in more detail below, the ligation may be direct or indirect. In other words, the ends of the padlock probe may be ligated directly to each other or they may be ligated to an intervening nucleic acid molecule/sequence of nucleotides. Thus the end regions of the padlock probe may be complementary to adjacent, or contiguous, regions in the cDNA product of step (a), or they may be complementary to non-adjacent (non-contiguous) regions of the cDNA (in which case, for ligation to occur, the “gap” between the two ends of the hybridized padlock probe is filled by an intervening molecule/sequence).

Upon addition to a sample, the ends of the padlock probe(s) hybridize to complementary regions in a cDNA molecule(s). Following hybridization, the padlock probe(s) may be circularized by direct or indirect ligation of the ends of the padlock probe(s) by a ligase enzyme. The circularized padlock probe is then subjected to RCA primed by the 3′ end of the cDNA (i.e. the RCA is target-primed). A DNA polymerase with 3′-5′ exonuclease activity is used. This permits the digestion of the cDNA strand in a 3′-5′ direction to a point adjacent to the bound padlock probe. Alternatively, the cDNA may be of appropriate length and may act as the primer for the DNA polymerase-mediated amplification reaction without such digestion. In this way the 5′ end of the RCP is advantageously continuous with the cDNA molecule. As a further alternative, instead of priming the RCA with the cDNA molecule, a separate primer that hybridizes to the padlock probe may be used in the reaction.

In some embodiments, the DNA polymerase is phi29. In additional embodiments, the phi29 enzyme or any other enzyme used herein has been modified or mutated to alter one or more properties such as stability (in the reaction or shelf-life during storage), activity, fidelity, processivity, speed, or specificity. In certain embodiments, methods involve an enzyme that is added to a sample or reaction. In some embodiments, there may be about, at least about, or at most about 0.1, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7. 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, 15.0, 15.5, 16.0, 16.5, 17.0, 17.5, 18.0, 18.5, 19.0. 19.5, 20.0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 410, 420, 425, 430, 440, 441, 450, 460, 470, 475, 480, 490, 500 U or U/μl (or any range derivable therein) of a specific enzyme such as phi29 (or a combination of enzymes) may added or used. Other enzymes that may be used in these amounts include, but are not limited to, ligase, reverse transcriptase, RNAse, and other polymerases.

It will be understood by the skilled person that ribonuclease digestion of RNA, hybridization of padlock probes to the cDNA, ligation of the padlock probes, and RCA may be carried out sequentially or simultaneously. Thus, for example, the ribonuclease, the padlock probe(s), the ligase, and the DNA polymerase for RCA may be added to the sample sequentially or substantially at the same time. Furthermore, any combination of steps of the method can be carried out simultaneously and are contemplated within the scope of the methods and composition described herein such that the RCP produced by the method is capable of detection and is indicative of the presence, absence and/or nature of an RNA in a sample. For example, ribonuclease digestion of RNA and hybridization of the padlock probe may be carried out simultaneously, or in the same step, or ligation of the padlock probe and RCA may be carried out simultaneously, or in the same step.

The “complementary regions” of the padlock probe correspond to the 5′ and 3′ end regions of the probe which hybridize to the cDNA. The padlock probe is thus designed to bind to the cDNA in a target-specific manner. The padlock probe may be designed to detect the presence of a particular RNA, for example to determine if a particular gene is expressed. It may also be designed for genotyping applications, for example to detect the presence of particular sequence variants or mutants in a cell or tissue sample—padlock probes may be designed which are specific for particular known mutants of genes (e.g. known mutations in the KRAS gene, as described further below) or for the wild-type sequence and accordingly may be used to detect or determine the presence, or the distribution (within the context of a tissue sample) of particular mutations or sequence variants, etc.

Accordingly, based on principles which are known in the art, a padlock probe may be designed to bind to the cDNA at a site selected to detect the presence of a particular sequence or sequence variant in the corresponding RNA. The probes may be designed and used to verify or confirm the presence of particular mutations or sequence variations (e.g. targeted genotyping) or they may be used on a sample with unknown mutation/variant status, to detect whether or not a mutation/variant is present, and/or the specific nature of the mutation/variant (blinded genotyping). For example a mixture of padlock probes may be used, one designed to detect the wild-type, and one more others designed to detect specific mutations/variants. For such genotyping applications, padlock probes may be designed to have identical complementary regions, except for the last nucleotide at the 3′ and/or 5′ end, which differs according to the genotype the probe is designed to detect; the DNA ligase which is used for circularization of the padlock probe does not accept mismatches when joining the ends of the padlock probe and hence ligation will only occur when the probe hybridizes to a sequence which it “matches” at the terminal nucleotide. In this way, single nucleotide differences may be discriminated.

In the hybridization reaction both ends of the padlock probe bind to the corresponding portion of, or region in, the cDNA such that they may become ligated, directly or indirectly, to each other resulting in circularization of the probe. Hybridization in this step does not require, but does include, 100% complementarity between the regions in the cDNA and the padlock probe. Thus “complementary”, as used herein, means “functionally complementary”, i.e. a level of complementarity sufficient to mediate a productive hybridization, which encompasses degrees of complementarity less than 100%. Thus, the region of complementarity between the cDNA and the region of the padlock probe may be at least 5 nucleotides in length, and is in some embodiments 10 or more nucleotides in length, e.g., 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50 or more nucleotides (and any range derivable therein). It may be up to 30, 40, 50, 60, 70, 80, 90 or 100 nucleotides in length (or any range derivable therein) in certain embodiments.

As noted above the ends of the padlock probe may be ligated directly or indirectly. “Direct ligation” of the ends of the padlock probe means that the ends of the probe hybridize immediately adjacently on the cDNA strand to form a substrate for a ligase enzyme resulting in their ligation to each other (intramolecular ligation). Alternatively, “indirect” means that the ends of the probe hybridize non-adjacently to the cDNA, i.e. separated by one or more intervening nucleotides. In such an embodiment the ends are not ligated directly to each other, but circularization of the probe instead occurs either via the intermediacy of one or more intervening (so-called “gap” or “gap-filling” (oligo)nucleotides) or by the extension of the 3′ end of the probe to “fill” the “gap” corresponding to the intervening nucleotides (intermolecular ligation). Thus, in the former case, the gap of one or more nucleotides between the hybridized ends of the padlock probe may be “filled” by one or more “gap” (oligo)nucleotide(s) which are complementary to the intervening part of the cDNA. The gap may be a gap of 1 to 60 nucleotides or a gap of 1 to 40 nucleotides or a gap of 3 to 40 nucleotides. In specific embodiments, the gap may be a gap of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 32, 35, 37, 40, 42, 45, 47, 50, 52, 55, 57 or 60 nucleotides, of any integer (or range of integers) of nucleotides in between the indicated values. In further embodiments, the gap may have a size of more than 60 nucleotides. In further embodiments, the gap between the terminal regions may be filled by a gap oligonucleotide or by extending the 3′ end of the padlock probe, e.g a gap oligonucleotide as defined herein above. Circularization of the padlock probe thereby involves ligation of the ends of the probe to at least one gap (oligo)nucleotide, such that the gap (oligo)nucleotide becomes incorporated into the resulting circularized probe. Hence, in such an embodiment the template for the RCA contains the padlock probe and the gap (oligo)nucleotide. In such an embodiment, the intervening part of the cDNA may be of any length sufficient to allow a productive hybridization with the gap oligonucleotide, wherein by “productive hybridization”, it is meant a hybridization capable of templating the indirect ligation (i.e. via the gap oligonucleotide) of the ends of the padlock probe. The padlock probe should be designed so that is does not contain any sequence which is complementary to the intervening part of the cDNA (i.e. the gap between the hybridized probe ends). The gap oligonucleotide may contain sequences useful for amplification or detection or sequencing, etc., of the eventual RCA product. Additionally or alternatively, the gap oligonucleotide may contain one or more tag or barcode sequences (discussed below). It will be seen that in a related embodiment more than one gap oligonucleotide might be used, which gap oligonucleotides hybridize to the intervening part of the cDNA in such a way that they, and the ends of the padlock probe, are ligated together end-to-end during the ligation step. In the latter case, the gap between the ends of the padlock probe hybridized to the cDNA may be filled by polymerase-mediated extension of the 3′ end of the padlock probe. Suitable polymerases are known in the art. Once the 3′ end has been extended as far as the 5′ end of the padlock probe, the ends may be joined in a ligation reaction. Hybridization of the probe and/or the (oligo)nucleotide to the cDNA is advantageously dependent on the nucleotide sequence of the cDNA thus allowing for the sensitive, specific, qualitative and/or quantitative detection of one or more cDNA, and by extension the corresponding RNA nucleotide sequences.

C. Samples

The methods and compositions disclosed herein may be used to evaluate RNA in any sample of cells in which an RNA molecule may occur, so long as the sample is amenable to in situ detection. A representative sample may comprise a fixed tissue section, a fresh frozen tissue or a cytological preparation comprising one or more cells. In certain embodiments, the formalin fixed paraffin embedded (FFPE) cells or tissue may be used. The sample may be permeabilized to render the RNA accessible. Appropriate means to permeabilize cells are well known in the art and include for example the use of detergents, e.g. appropriately diluted Triton X-100 solution, e.g. 0.1% Triton X-100, or Tween, 0.1% Tween, or acid treatment e.g. with 0.1M HCl. Permeabilization of tissue samples may also comprise treatment of the sample with one or more enzymes, e.g. pepsin, proteinase K, trypsinogen, or pronase, etc. Also, microwave treatment of the sample may be carried out as described in the art.

The sample may also be treated to fix RNA contained in the cells to the sample, for example to fix it to the cell matrix. Such procedures are known and described in the art. For example, in the field of in situ hybridization, reagents are known for fixing mRNA to cells. In particular, 5′ phosphate groups in the RNA may be linked to aminespresent on proteins in the cellular matrix via EDC-mediated conjugation (EDC: 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide), thus helping to maintain the localization of the RNA relative to other cellular components. Such a technique has previously been described in relation to microRNAs and their detection via in situ hybridization (Pena et al., 2009).

In certain embodiments, a sample is fixed with formalin. In addition to or instead of formalin, a sample may be fixed with formaldehyde, ethanol, methanol, and/or picric acid. In other embodiments, a sample may be fixed in a non-formalin-based solution, such as Carnoys, Modified Carnoys/Clarkes solution, Ethanol, FineFX, Methacarn, Methanol, Molecular Fixative (UMFIX), BoonFix, Polyethylene glycol based fixatives, RCL2, Uni-Fix, Glyco-Fix, Gluteraldehyde, HistoCHOICE, HistoFix, HOPE Fixation, Ionic liquid, Mirsky's fixative, NOTOXhisto, Prefer, Preserve, or Zenker. See NHS “Evidence Review: Non-formalin fixatives” August 2009, which is hereby incorporated by reference. In additional embodiments, fixation techniques include fixation in acetone, methanol, ethanol, methanol acetone (e.g., fix in methanol, remove excess methanol, permeabilize with acetone), methanol-acetone mix (e.g., 1:1 methanol and acetone mixture), methanol-ethanol mix (e.g., 1:1 methanol and ethanol mixture), formalin, paraformaldehyde, gluteraldehyde, Histochoice, Streck cell preservative (Streck Labs., Nebraska), Bouin's solution (a fixation system containing picric acid), and/or Sed-Fix (a polyethylene glycol based fixation system available from Leica Biosystems, Buffalo Grove Va.), FineFix (Leica Biosystems, Buffalo Grove Va.).

Pieces of tissue may be embedded in paraffin wax to increase their mechanical strength and stability and to make them easier to cut into thin slices.

Permeabilization involves treatment of cells with (usually) a mild surfactant. This treatment will dissolve the cell membranes, and allow larger dye molecules access to the cell's interior.

In additional embodiments, a sample may be stained before or after contact with one or more padlock probes. In some instances, a sample is stained with a cytological stain such as hematoxylin and eosin (H & E), gram staining, Ziehl-Neelsen staining, Papanicolaou staining, period acid-Schiff (PAS), Masson's trichrome, Romanowsky stains, Wright's stain, Jenner's stain, May-Grunwald stain, Leishman stain, Giemsa stain, silver staining, Sudan staining or Conklin's staining. In certain embodiments, sample may be stained specifically with one or more of acridine orange, Bismarck brown, carmine, coomassie blue, crystal violet, DAPI, eosin, ethidium bromide, acid fuchsine, Hematoxylin (or haematoxylin), Hoechst stains, iodine, Malachine green, methyl green, methylene blue, neutral red, Nile blue, Nile red, osmium tetroxide, rhodamine, and safranin.

D. Localized In Situ Detection

The next step of the method following the RCA step is to determine the presence of the extended product (i.e. the RCA product or RCP) in the reaction mixture in order to detect the target RNA in the sample. In other words, the sample is screened, etc. (i.e., assayed, assessed, evaluated, tested, etc.) for the presence of any resultant RCP in order to detect the presence of the target RNA in the sample being tested. The RCP produced by the methods described herein may, in the broadest sense, be detected using any convenient protocol. The particular detection protocol may vary depending on the sensitivity desired and the application in which the method is being practiced. In one embodiment, the RCP detection protocol may include an amplification component, in which the copy number of the RCA product (or part thereof) is increased, e.g., to enhance sensitivity of the particular assay, but this is not generally necessary. Thus the RCP may be directly detected without any amplification.

The localized detection may be viewed as comprising two steps, firstly the development of a detectable signal and secondly the read-out of the signal. With respect to the first step, the following detection methods could be contemplated. The signal may include, but is not limited to a fluorescent, chromogenic, enzymatic, radioactive, luminescent, magnetic, electron density or particle-based signal. Thus, a label directly or indirectly providing such a signal may be used. The signal could be obtained either by incorporating a labeled nucleotide during amplification to yield a labeled RCP, using a complementary labeled oligonucleotide that is capable of hybridization to the RCP (a “detection probe”), or to, in a sequence non-specific manner, label the produced nucleic acid. The label could be direct, (e.g. but not limited to: a fluorophore, chromogen, radioactive isotope, luminescent molecule, magnetic particle or Au-particle), or indirect (e.g. but not limited to an enzyme or branching oligonucleotide). The enzyme may produce the signal in a subsequent or simultaneous enzymatic step. For example horseradish peroxidase may be provided as a label that generates a signal upon contact with an appropriate substrate. Several methods are well described in the literature and are known to be used to render signals that are detectable by various means (which may be used in the second step), e.g. microscopy (bright-field, fluorescent, electron, scanning probe), flow cytometry (fluorescent, particle, magnetic) or a scanning device.

In a particular embodiment, detection is by means of labeled oligonucleotide probes (“detection probes”) which have complementarity, and thereby hybridize, to the RCP. Such labeling may be by any means known in the art, such as fluorescent labeling including ratiolabeling, radiolabeling, labeling with a chromogenic or luminescent substrate or with an enzyme e.g. horseradish peroxidase, etc. Fluorescently-labeled probes are employed in some embodiments. In other embodiments, a chromogenic label is employed. The signal produced by the labels may be detected by any suitable means, such as visually, including microscopically. In particular embodiments, a signal amplification technique or system may be used in conjunction with label detection. With such techniques or systems, the signal from a label may be amplified. In certain embodiments, signal amplification involves tyramide. Tyramide has been used to amplify chromogenic and fluorescent signals. In certain embodiments, a tyramide amplification system is used, which is commercially available from Perkin Elmer.

In some embodiments, detection of the label may be direct or it may involve several additional steps and/or reagents to detect the label indirectly. The label may be an enzyme capable of direct detection in the presence of an additional reagent, such as a substrate. Alternatively, and as discussed in further detail below, the label may be detected indirectly through the addition of one or more substances that bind to or react with the label. In some embodiments, for example, such a substance is an antibody or antibody fragment that specifically binds to the label. The antibody or antibody fragment may itself be labeled or it may be detected by the binding of a secondary antibody that itself may or may not be labeled with a detectable moiety. A person of ordinary skill in the art is well aware of a variety of ways of labeling a detection probe. In some embodiments, the crosslinking technology or linkers discussed above may be employed to join a label to a detection probe.

As the RCPs are comprised of repeated “monomers” corresponding to the padlock probe (optionally with additional incorporated nucleotides or gap oligonucleotides, as discussed above), the sequences to which the oligonucleotide probes hybridize will be “repeated,” i.e. assuming the RCA reaction proceeds beyond a single replication of the template, multiple sites for hybridization of the oligonucleotide probes will exist within each RCP. In this way, the signal intensity from the label on the oligonucleotide probes may be increased by prolonging the RCA reaction to produce a long RCA product containing many hybridization sites. Signal intensity and localization is further increased due to spontaneous coiling of the RCP. The resulting coils, containing multiple hybridized oligonucleotide probes, give a condensed signal which is readily discernible by, for example, microscopic visualization against a background of non-hybridized oligonucleotide probes. Hence, it may be possible qualitatively or quantitatively to detect the RNA(s) in a sample without performing a washing step to remove unhybridized oligonucleotide probes.

Multiplexed detection may be facilitated by using differently-labeled oligonucleotide probes for different RNAs, wherein the respective oligonucleotide probes are designed to have complementarity to “unique” sequences present only in the RCPs (corresponding to sequences present only in the padlock probes) for the respective RNAs. Such sequences may be barcode or tag sequences, as discussed above. In a particular embodiment, two or more differentially labeled detection oligonucleotides may be used to detect one or more RCPs, one labeled detection oligonucleotides reporting the wild-type variant of a gene and another labeled detection oligonucleotide(s) reporting one or more mutant variants of the gene. Different fluorophores may be used as the labels. Multiplexed detection can also be achieved by applying in situ sequencing technologies such as sequencing by ligation, sequencing by synthesis, or sequencing by hybridization.

The present method allows for single nucleotide resolution in the detection of RNA nucleotide sequences. The present method may thus be used for the detection of one or more point mutations in an RNA or indeed any single-nucleotide variant. Thus the method may find utility in the detection of allelic variants or alternative splicing, etc. The superior sensitivity and localization afforded by the method also means that it may be used to detect RNA in single cells. For example, multiplex detection of mRNA transcripts in some embodiments may advantageously be used for expression profiling, including in a single cell.

In some embodiments, replication or amplification of a padlock probe may involve incorporation of a labeled nucleotide that may be specific to one padlock probe so detection of that specific label identifies the sequence of the padlock probe and the sequence complementary to the padlock probe.

In certain embodiments, a probe is labelled with a detection moiety that can be specifically recognized and/or bound by another agent or substance, which may be referred to as a detection label substance. Such detection moieties or detection labels involve, but are not limited to, antibodies or antibody fragments, haptens or poly haptens, synthetic peptides, antigenic nucleic acid sequences, sequence-specific DNA binding proteins, sequence specific DNA protein complexes, and PNA/DNA hybrids.

Antibodies are used in certain embodiments. For instance, in some aspects, a polyclonal rabbit IgG is employed. Rabbit immunoglobulins may be covalently linked to detection oligos that are labelled with amino groups at their 5′ and/or 3′ end(s) via crosslinkers with an amine reactive functional groups—such as N-hydroxysucccinmide (NHS) esters. The antibody-labelled oligo can then be detected using a polyenzyme-anti-rabbit antibody conjugate such as goat anti-rabbit poly-alkaline phosphatase (goat α rabbit poly-AP or goat anti-rabbit poly-horseradish peroxidase (goat α rabbit poly-HRP). Suitable crosslinkers are available from suppliers such as Thermofisher or Solulink. Goat anti-Rabbit polyenzyme conjugates are available from Leica Biosciences. It will be understood to those in the art that antibodies that may be used for detection in human cells and tissues include those from chickens, goats, guinea pigs, hamsters, horses, mice, rats, and sheep. IgG antibodies may be obtained from these animal sources. Other examples can be found in U.S. Pat. No. 6,942,972, Bioconjugate Techniques, Second Edition, Academic Press/Elsevier by Greg T. Hermanson (ISBN 978-0-12-370501-3), Solulink White Paper: “Protein oligonucleotide conjugate synthesis made easy, efficient and reproducible,” all of which are hereby incorporated by reference.

In some embodiments, a detection tag may be an antibody fragment, such as an IgG Fc fragment. As discussed above, fragments of antibodies from chickens, goats, guinea pigs, hamsters, horses, mice, rats, or sheep may be employed in embodiments discussed herein. For example, a rabbit IgG Fc fragment might be used. This can be employed by covalently attaching the antibody fragment to a detection oligo and using a polyenzyme labelled anti-rabbit Fc fragment-specific antibody to effect detection. This may give a cleaner result than using a whole antibody. Systems could also be designed using alternative antibody fragments such as F(ab′)₂ fragments. Antibody fragments include that that may be obtained from the antibodies discussed in the references above. In some embodiments, an antibody fragment is a recombinant antibody fragment. Such a fragment has the potential to give very low background staining. It would be possible to produce a monoclonal antibody and use a fragment of it for detection assays.

A variety of haptens may be employed, including those in which commercial antibodies are readily available, such as Alexaflour, Biotin, BODIPY (boron-dipyrromethene), Cascade blue, Dansyl, Digoxygenin, Dinitrophenol (DNP), Lucifer Yellow, Oregon Green, Rhodamine, Streptavidin, TAMRA (tetramethyl rhodamine), and Texas Red. For instance, fluorescein can be incorporated at the 3′ and 5′ ends of detection oligos during synthesis. Anti-fluorescein antibodies are commercially available and can be detected using Leica BioSystems standard detection system. Additionally, poly haptens may be employed in conjunction with a detection oligo. Polyethylene glycol (PEG) is an example of a poly hapten For instance, in some embodiments, detection oligos are conjugated to PEG. The repeating units of PEG can then be bound by an anti PEG antibody (which are available commercially from suppliers such as Epitomics and Life Sciences Inc). A degree of amplification can be achieved depending upon how many PEG repeating units are bound by antibody. Jäschke J, Fürste J P, Nordhoff E, Hillenkamp F, Cech, and Erdmann V A. Synthesis and properties of oligodeoxyribonucleotide-polyethylene glycol conjugates. Nucleic acids Research 1994: 22 (22) 4810-4817, which is hereby incorporated by reference. Other examples include attaching known haptens to a polymer with suitable functional groups in its repeating units (e.g the repeating amine groups in poly-lysine or the repeating carboxylate groups in poly-glutamic acid). In some embodiments the attachment is polyacrylamide hydrazide or various poly-amino acids (poly-arginine, poly-asparagine, poly-aspartic acid, poly-glutamic acid. poly-glutamine and poly-lysine) as possible backbone/scaffold molecules to which haptens can be attached. A hapten that may be used includes, but is not limited to, dinitrophenol, biotin, digoxygenin, fluorescein and rhodamine, as well as oxazole, pyrazole, thiazole, nitroaryl, benzofuran, triterpen, urea, thioureas, rotenoid, coumarin or cytolignin, any of which might be suitable for attachment to the polymeric backbone.

Synthetic peptides may also be used in detection methods. Peptides that may be attached to a detection probe would be those that could be specifically recognized and/or bound by a detection label substance. In some embodiments, the synthetic peptide is YPYDVPDYA (from influenza hemaglutinin), HHHHHH (6× His or His tag), DYKDDDDK (the FLAG® peptide), all of which are recognized by antibodies that are commercially available from Origene. In other embodiments, the synthetic peptide is HHHHHHGS (6× His variant) recognized by Millipore's antibody Clone 4D11 or ATDYGAAIDGF (from Phage M13 Coat protein g3p), which is recognised by Anti-g3p (pIII) available from MoBiTec.

Peptides can be conjugated to oligonucleotides using the same chemistry as that used for antibodies (see above). A huge variety of peptide specific antibodies are commercially available. Most of those in the LBS range are unsuitable as they are directed at targets that occur in human cells. It would be better to use a non-biological peptide sequence—or a sequence from a protein of plant or prokaryotic origin. However, LBS could design and produce bespoke anti-peptide antibodies for use in detection systems. See Lass-Napiorkowska A, Heyduk E, Tian L and Heyduk T. Detection methodology based on target molecule-induced sequence-specific binding to a single-stranded oligonucleotide. Analytical Chemistry 2012: 84 (7) 3382-3389, which is hereby incorporated by reference.

In further embodiments, a detection label that is attached to a detection probe is an antigenic DNA sequence. In an aspect of methods described herein, a detection label may be an E2 site 25 from the human papilloma virus(HPV) sequence DNA, i.e. 5′-GTAACCGAAATCGGTTGA-3′ (SEQ ID NO:113). Raising antibodies that recognize specific DNA sequences may be technically difficult. An approach that has worked involved a highly stable DNA protein complex as an immunogen. Such antibodies can be used in conjunction with a cognate sequence in the context of a detection probe for padlock probes. See Cerutti M L, Centeno J m Goldbaum F A and de Prat-Gay G. Generation of sequence-specific high affinity anti-DNA antibodies. J. of Biochemistry 2001 276 (16) 12769-12773, which is hereby incorporated by reference.

In additional embodiments a detection tag may involve a sequence-specific DNA binding protein. In some embodiments, the protein is all or part of the E2 protein from HPV 16, Tet repressor (from Gram negative bacteria), Tet repressor (from Gram negative bacteria), or GAL 4 (from yeast). This can be implemented by incorporating one strand of the recognition sequence for the DNA binding protein into the padlock probe and the complementary sequence into the detection probe. The RCA products are incubated with a cocktail of the DNA binding protein, the detection oligo and antibody that will recognise the DNA-binding protein the. Antibodies to Tet repressor are commercially available (from Gen Way Biotech for example). Antibodies to E2 have been described by Cerutti et al. Care should be taked to avoid the use of a protein that has significant non-specific DNA-binding activity. See Cerutti et al., Journal of Biochemistry, 2001, 276 (16) 12769-12773 and Pook et al., European Journal of Biochemistry, 1998, 258 915-922, both of which are hereby incorporated by reference.

Alternatively, sequence specific DNA protein complexes may be employed in detection methods. For instance the following complexes may be employed: E2 protein/E2 site 25 DNA—complex; Tet repressor/tet operator complex. This involves the use of antibodies that specifically recognize the complex between a DNA-binding protein and its cognate sequence, or specifically recognise the conformation of the DNA-bound form of the protein. This approach has the potential to circumvent problems that might be caused by non-specific DNA binding. See Cerutti et al., Journal of Biochemistry, 2001, 276 (16) 12769-12773 and Pook et al., European Journal of Biochemistry, 1998, 258 915-922, both of which are hereby incorporated by reference.

In certain embodiments, the detection label or tag may involve a PNA/DNA hybrid. Peptide Nucleic Acids (PNA) form extremely stable hybrids with DNA or RNA. Antibodies have been developed that recognise the backbone conformation (rather than the sequence of such hybrids). It is therefore possible to design a system whereby the detection oligo consists of PNA. Once this has hybridized to its target it can be detected by a PNA/DNA—specific antibody, which can in turn be recognized by one of Leica BioSystems standard detection systems. See e.g., U.S. Pat. No. 5,612,458, which is hereby incorporated by reference.

In addition, in some embodiments a detection moiety may be specifically recognized or bound by non-antibody proteins or protein domains that mediate specific high-affinity interactions. The group includes, for instance, protein structures comprising ankyrin-repeats. Typically, in designed ankyrin-repeat proteins (DARPins) three, four or preferably five repeat ankyrin motifs are present. These may form a stable protein domain with a large potential target interaction surface. Further details may be derived, for example, from Binz et al., 2003, J Mol Biol.; 332(2): 489-503, which is incorporated herein by reference.

A further example of a specific, highly affine molecule is an affibody molecule, i.e. a protein based on the Z domain (the immunoglobulin G binding domain) of protein A. In contrast to antibodies, affibody molecules are typically composed of alpha helices and lack disulfide bridges. They may be expressed in soluble and proteolytically stable forms in various host cells. Affibody molecules may further be fused with other proteins. Further details may be derived, for example, from Nord et al., 1997, Nat Biotechnol.; 15(8): 772-777, which is incorporated herein by reference.

The group of highly affine protein interactors also comprises adnectins. Adnectins are based on the structure of human fibronectin, in particular its extracellular type III domain, which has a structure similar to antibody variable domains, comprising seven beta sheets forming a barrel and three exposed loops on each side corresponding to the three complementarity determining regions. Adnectins typically lack binding sites for metal ions and central disulfide bonds. They are approximately 15 times smaller than an IgG type antibody and comparable to the size of a single variable domain of an antibody. Adnectins may be customized in order to generate and/or increase specificity for target molecules by modifying the loops between the second and third beta sheets and between the sixth and seventh sheets. Further details may be derived, for example, from Koide and Koide, 2007, Methods Mol Biol.; 352: 95-109, which is incorporated herein by reference.

A further example is the antibody mimetic anticalin, which is derived from human lipocalin. Anticalins typically have the property of binding protein antigens, as well as small molecule antigens. They are composed of a barrel structure formed by 8 antiparallel beta sheets, connected by loops and an attached alpha helix. Mutagenesis of amino acids at the binding site may allow for changing of affinity and selectivity of the molecule. Further details may be derived, for example, from Skerra, 2008, FEBS J., 275 (11): 2677-83, which is incorporated herein by reference.

Another example is affilin, i.e. a genetically engineered protein with the ability to selectively bind antigens, which is structurally derived from gamma-B crystallin or from ubiquitin. Affilins are typically constructed by modification of near-surface amino acids of gamma-B crystallin or ubiquitin and isolated by display techniques such as phage display. The molecular mass of crystallin and ubiquitin based affilins is typically about one eighth or one sixteenth of an IgG antibody, respectively. This may lead to heat stability up to 90° C. and an improved stability towards acids and bases. Further details may be derived, for example, from Ebersbach et al., 2007 J Mol Biol.; 372(1): 172-185 or from Hey et al., 2005, Trends Biotechnol.; 23(10): 514-522, which are incorporated herein by reference.

The group of highly affine protein interactors also comprises avimers, i.e. artificial proteins that are able to specifically bind to certain antigens via multiple binding sites. Typically, the individual avimer sequences are derived from A domains of various membrane receptors and have a rigid structure, stabilized by disulfide bonds and calcium. Each A domain can bind to a certain epitope of the target molecule. The combination of domains binding to different epitopes of the same target molecule may increases affinity to this target. Further details may be derived, for example, from Silverman et al., 2005, Nat Biotechnol.; 23(12): 1556-61, which is incorporated herein by reference.

Other embodiments include knottins, i.e. small disulfide-rich proteins characterized by a special disulfide through disulfide knot. This knot is typically obtained when one disulfide bridge crosses the macrocycle formed by two other disulfides and the interconnecting backbone (disulfide III-VI goes through disulfides I-IV and II-V). Knottin peptides could be shown to bind with high affinity (about 10 to 30 nmol/L) to integrin receptors. The knottin scaffold may accordingly be used for the design of highly affine molecules which are able to bind detection moieties according to the invention. Further details may be derived, for example, from Kimura et al., 2009, Cancer Res., 69; 2435, which is incorporated herein by reference.

The group of highly affine protein interactors additionally comprises fynomers, i.e. Fyn SH3-derived proteins .Fyn is a 59-kDa member of the Src family of tyrosine kinases. The Fyn SH3 domain comprises 63 residues, and its amino acid sequence is fully conserved among man, mouse, rat, and monkey. Fynomers are typically composed of two antiparallel beta sheets and contain two flexible loops (RT and n-Src loops) to interact with other proteins or targets. Further details may be derived, for example, from Grabulovski et al., 2007, Journal of Biological Chemistry, 282 (5): 3196-3204, which is incorporated herein by reference.

Yet another example of a specific, highly affine molecule is a phylomer peptide. Phylomer peptides are bioactive fragments of naturally occurring proteins that are encoded in the genomes of evolutionary diverse microbes, which are partially sourced from extreme environments and may have evolved over billions of years, providing a multitude of distinct and stable structures capable of binding to biological molecules. Further details may be derived, for example, from Watt, 2009, Future Med. Chem., 1(2): 257-265, which is incorporated herein by reference.

The group of highly affine protein interactors also comprises kunitz domain peptides. Kunitz domains are the active domains of Kunitz-type protease inhibitors. They typically have a length of about 50 to 60 amino acids and a molecular weight of 6 kDa. Examples of Kunitz-type protease inhibitors are aprotinin, Alzheimer's amyloid precursor protein (APP), and tissue factor pathway inhibitor (TFPI). Kunitz domains are stable as standalone peptides and are able to recognize specific targets such as protein structure and may accordingly be used for the design of highly affine molecules which are able to bind detection moieties according to the invention. Further details may be derived, for example, from Nixon and Wood, 2006, Curr Opin Drug Discov Devel, 9(2), 261-268, which is incorporated herein by reference.

Other detection methods may be employed. In some embodiments, Förster (Fluorescence) resonance energy transfer (FRET) may be implemented to detect the presence or absence of a particular sequence. Examples can be found in Li et al., Biochem Biophys Res Commun. 2008 Sep. 5; 373(4):457-61, which is hereby incorporated by reference.

Any probe described herein may be multiply labeled with one or more of the same or different labels. In some cases, a probe may be multiply labeled with the same label. For example, branched probes may be used in which one or more labels is attached on each branch. In some embodiments, a branched DNA (bDNA) signal amplification technique is used involving sets of labeled probes, hybridized sequentially to the target nucleic acid creating comb-like DNA structures, which generate chromogenic or fluorescent signals. See Murphy et al., J Clin Microbiol, 1999 March; 37(3):812-4, Player et al., J Histochem Cytochem, 2001 May; 49(5):603-12, and Collins et al., Nucl. Acids Res., (1997) 25 (15): 2979-2984, which are all incorporated by reference. In further embodiments, tyramide signal amplification (TSA) may be employed. TSA is based on the ability of horseradish peroxidase (HRP) to convert fluorescent or hapten-labeled tyramide molecules into a highly reactive oxidized intermediate that can bind tyrosine at the site of the HRP-probe binding site. See Speel E J, Nucl. Acids Res. (1997) 25 (15): 2979-2984, Thompson et al., Neuron, 60(6), 1010-1021, Werner et al., Prog Histochem Cytochem., 2001; 36(1):3-85, and Qian et al., Diagn Mol Pathol., 2003 March; 12(1):1-13, all of which are hereby incorporated by reference.

In certain embodiments, multiple padlock probes or detection probes may be employed. It is contemplated that in some embodiments, probes are detected serially instead of at the same time. In cases where probes are added serially, they may be detected serially and there may be a step in between in which detection of a previously added probe is eliminated after it has already been detected. An example of this might be achieved using photobleaching. For example, a first probe may be detected and then the probe may be photobleached prior to addition of a second probe that is then detected. Photobleaching refers to the photochemical destruction of a fluorophore. In the context of FRET, phobleaching may involve the acceptor or the donor molecule. Additional embodiments may involve fluorescence recovery after photobleaching (FRAP).

In some embodiments, a labeled nucleotide is incorporated directly into a probe that is either the padlock probe or the detection probe. In certain embodiments, the labeled nucleotide is incorporated in the detection probe, while in other embodiments labeled nucleotides are incorporated into the amplification product.

Oligonucleotides and dNTPs may be labelled with a variety of substances including radioactive isotopes (such as ¹³C, ³H, ³²P, ³⁵S), haptens (such as organic fluorescent dyes, biotin, digoxigenin (DIG), dinitrophenyl (DNP)), or enzymes (such as calf intestinal alkaline phosphatase or HRP). Haptens are small molecules that can illicit an immune response only when coupled to a larger carrier molecule, such as a protein. Hapten labels are usually used for indirect detection methods in combination with streptavidin or antibody conjugates (as discussed above). Fluorescent labels are used for direct detection.

Nucleotide analogs are routinely used to label, isolate, study, and manipulate DNA in a wide variety of applications. These nonradioactive nucleotide analogs are introduced into a DNA strand by chemical and enzymatic 5′ and 3′ end labeling and through internal enzymatic labeling or post-labeling methods. The ability to incorporate modified nucleotides into a growing chain of dNTPs is dependent upon a number of factors including the DNA polymerase (especially its fidelity), size and type of fluorophore, the linker between the nucleotide and the fluorophore, and position for attachment of the linker and the cognate nucleotide. In some embodiments, a polymerase that contains a strong 3′ to 5′ exonuclease activity (proofreading ability) is not used for incorporating nucleotide analogs. (Jon P. Anderson et al, (BioTechniques, Vol. 38, No. 2, February 2005, pp. 257-264, which is incorporated by reference). However, according to patent application US 2011/0244548 A1, which is incorporated by reference, Life Technologies have developed several novel DNA polymerases that have reduced discrimination against the incorporation of one or more fluorescently labeled nucleotides into DNA/polynucleotides. Furthermore, various sequencing by synthesis methods (used by Helicos and Illumina) use the incorporation of fluorescent dye terminators whereby a single fluorophore labeled “terminator/inhibitory” nucleotide is incorporated per cycle. Excitiation of individual fluorophores by laser is recorded. Fluorophore and terminator/inhibitory group are then removed allowing addition of the next nucleotide.

Nucleotide incorporations can be detected through fluorescence resonance energy transfer (FRET) interactions between a fluorophore-bearing polymerase and .gamma.-phosphate-labeled nucleotides, or with zeromode waveguides. The illumination can be restricted to a zeptoliter-scale volume around a surface-tethered polymerase such that incorporation of fluorescently labeled nucleotides can be observed with low background (Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682-686 (2003); Lundquist, P. M. et al. Parallel confocal detection of single molecules in real time. Opt. Lett. 33, 1026-1028 (2008); Korlach, J. et al. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl. Acad. Sci. USA 105, 1176-1181 (2008), the disclosures of which are incorporated herein by reference in their entireties).

In addition to what is described above, further embodiments related to detection probe and detection systems are discussed below. U.S. Pat. No. 8,114,973 describes optically labeled nucleotides. U.S. Pat. No. 8,133,702 describes fluorescent dye labeled nucleotides. The Alex Fluor dyes (Molecular Probes) are widely used to fluorescently label nucleotides. U.S. Pat. No. 7,235,361 describes fluorescent semiconductor nanocrystals (quantum dots) which can be associated with compounds, including nucleotides. These U.S. patent cited above are all specifically incorporated by reference. Nucleotides labeled with quantum dots are available from Life Technologies. In other embodiments, detection methods may employ quantum dots, which refer to semiconductor nanocrystals that have broad excitation spectra, narrow emission spectra, tunable emission peaks, long fluorescence lifetimes, negligible photobleaching, and the ability to be conjugated to biomolecules, such as probes. See Barroso, J Histochem Cytochem. 2011 March; 59(3):237-51, which is hereby incorporated by reference. Other references that describe the use of labeled nucleotides are incorporated by reference; these include the following references discussing radiolabelled nucleotides (Yan et al., Biochem Biophys Res Commun, 2001 Jun. 8; 284(2):295-300; von Guggenberg et al., Cancer Biother Radiopharm., 2010 December; 25(6):723-31, Tang et al, Biotechniques, 2006 June; 40(6):759-63, all of which are incorporated by reference); fluorescently labeled nucleotides (Bethge et al., Org Biomol Chem, 2010 May 21; 8(10):2439-48, Linck et al., Photochem Photobiol, 2012 Feb. 23. doi: 10.1111/j.1751-1097.2012.01119.x, Knapp et al., Chemistry, 2011 Mar. 1; 17(10):2903-15, Linck et al., European J. Medicinal Chemistry, 2010; 45(12):5561-6, Jarchow-Choy et al., Nucleic Acids Res, 2011 March; 39(4):1586-94, which are all incorporated by reference); enzyme-conjugated oligonucleotides (Ghosh et al., Bioconjug Chem, 1990 January-February; 1(1):71-6, van de Corput et al., J Histochem Cytochem, 1998 November; 46(11):1249-59, which are hereby incorporated by reference); antibody-conjugated oligonucleotides (Kazane et al., Proc Natl Acad Sci USA, 2012 Mar. 6; 109(10):3731-6. Han et al., Bioconjug Chem, 2010 Dec. 15; 21(12):2190-6, which are hereby incorporated by reference); biotin- or streptavidin-conjugated nucleotides (Rabe et al., Molecules, 2011 Aug. 15; 16(8):6916-26, which is hereby incorporated by reference); DIG-conjugated nucleotides (Kriegsmann et al., Histochem Cell Biol, 2001 September; 116(3):199-204, Jalabi et al., J Histochem Cytochem, 2003 July; 51(7):913-9, Escarceller et al., Anal Biochem, 1992 October; 206(1):36-42, Trayhurn et al. Anal Biochem, 1994, October; 222(1):224-30, which are hereby incorporated by reference); DNP conjugated nucleotides (Horáková et al., Org Biomol Chem, 2011 Mar. 7; 9(5):1366-71, Keller et al., Anal. Biochem, 1989 March; 177(2):392-5, all of which are incorporated by reference); quantum dot labelled nucleotides (He et al., Biomaterials, 2011 August; 32(23):5471-7, Bakalova et al., J Am Chem Soc, 2005 Aug. 17; 127(32):11328-35, Ma et al., Chromosoma, 2008 April; 117(2):181-7, Barrett et al., Nanoscale, 2011 August; 3(8):3221-7. Zhang et al., Faraday Discuss, 2011; 149:319-32; discussion 333-56, which are hereby incorporated by reference); nanoparticle-conjugated nucleotides (Zheng et al., J Am Chem Soc, 2008 Jul. 30; 130(30):9644-5; Lee et al., “Multiplexed detection of oligonucleotides with bio-barcoded gold nanoparticle probes,” in Methods in molecular biology (Clifton, N.J.), 2011—Springer-Verlag, all of which are hereby incorporated by reference); metal-conjugated oligonucleotides (Oser et al., Nucleic Acids Res, 1988 Feb. 11; 16(3):1181-96, Wei et al., Anal. Bioanal Chem, 2012 January; 402(3):1057-63, Gasser et al., Dalton Trans 2011 Jul. 21; 40(27):7061-76, which are all incorporated by reference); and, PNAs (Gasser et al., Dalton Trans, 2012 Feb. 28; 41(8):2304-13, which is hereby incorporated by reference). More details regarding detection methods can be found in Olesen et al., Biotechniques, 1993 September; 15(3):480-5, Suzuki et al., Anal. Biochem, 1993 May 1; 210(2):277-81, Chai et al., Anal. Chim Acta, 2012 Feb. 17; 715:86-92, all of which are hereby incorporated by reference.

A variety of embodiments involve sequencing one or more nucleic acids. In some embodiments, after a padlock probe is amplified or replicated, the rolling circle amplification product is sequenced. In some embodiments, a nucleic acid is sequenced on a slide or in the same physical context that one or more other reactions occurred, such as replication. In other embodiments, a nucleic acid is removed from a slide or from the physical context under which a previous enzymatic reaction (via an exogenously added enzyme) occurred according to methods described in embodiments, such as transcribing using reverse transcriptase, ligating, or replication. For example, cells on a slide or a tissue sample on a slide may be physically removed from the slide. In some embodiments, the cells or tissue are placed in a tube and are no longer attached or fixed to a physical surface or support. A sequencing reaction may occur on a physical or solid support or it may be performed in solution.

Sequencing-by-synthesis involves the template-dependent addition of nucleotides to a template/primer duplex. Traditional sequencing-by-synthesis is performed using dye-labeled terminators and gel electrophoresis (so-called “Sanger sequencing”). See, e.g., Sanger, F. and Coulson, A. R., 1975, J. Mol. Biol. 94: 441-448; Sanger, F. et al., 1977, Nature. 265(5596): 687-695; and Sanger, F. et al., 1977, Proc. Natl. Acad. Sci. U.S.A. 75: 5463-5467, both of which are hereby incorporated by reference. In other embodiments, a terminator nucleotide may be employed, which may be labeled. In some embodiments, sequencing is accomplished using high-resolution electrophoretic separation of resulting single-stranded extension products in a capillary-based polymer gel or by mass spectroscopy.

Single molecule sequencing methods have been proposed that provide increased resolution, throughput, and speed at reduced cost. For example, a sequencing-by-synthesis method that results in sequence determination without consecutive base incorporation, has been proposed by Braslaysky, et al., Proc. Nat'l Acad. Sci., 100: 3960-3964 (2003), which is hereby incorporated by reference. These methods do not rely on the user of terminator nucleotides as in Sanger sequencing. Instead, template/primer duplex is anchored directly, or indirectly (e.g., via a polymerase enzyme) to a surface and labeled nucleotides are added in a template-dependent manner.

In addition to Sanger sequencing, sequencing may also occur by “iterative cycles of enzymatic manipulation and imaging based data collection.” Shendure et al., Nature Biotech., 2008, 26(10):1135-1145, which is hereby incorporated by reference. These second generation technologies may be categorized as follows: (1) microphoretic techniques; (2) sequencing by hybridization; (3) observation of single molecules in real time; and, (4) cyclic array sequencing. Commercial embodiments of high-throughput sequencing technology include 454 sequencing (Roche Applied Sciences), Solexa (Illumina), SOLiD (Applied Biosystems), the Polonator (Dover/Harvard), Helioscope™ Single Molecule Sequencer technology (Helicos), Massively Parallel Signature Sequencing (MPSS) (Lynx Therapeutics), Ion semiconductor sequencing (Ion Torrent), DNA nanoball sequencing (Complete Gneomics), Single molecule SMRT™ sequencing (Pacific Biosciences), Single molecule real time (RNAP) sequencing, and Nanopore DNA sequencing. Any of the sequencing technologies discussed above may be modified or applied so as to obtain sequence information from a sample that has undergone rolling circle amplication of one or more padlock probe to detect or identify nucleic acid sequence(s). One or more aspects of the sequencing technology may be performed while a sample remains on a solid support or it may occur in solution, such as after the sample has been removed from a solid support or has been otherwise disrupted on the solid support.

It is contemplated that in certain embodiments, any sequencing that is performed in conjunction with padlock probe technology is automated. In other embodiments, while aspects of methods may be autormated, others may not be. In some embodiments it is contemplated that sequencing may be performed in situ on a solid support or that enzymatic or chemical reactions prior to sequencing may occur in situ on a solid support (such as addition of chain terminating nucleotides). In other embodiments, separation or isolation of a nucleic acid to be sequenced occurs in solution or not in situ or not on the solid support used for rolling circle amplification. In further embodiments, identification of a sequence does not occur in situ or does not occur on the solid support that was used for rolling circle amplication. In certain embodiments, a solid support used for rolling circle amplification may be moved to a different machinery or location in order to do all or part of a sequencing reaction. In particular embodiments, sequencing involves a machine for electrophoretic separation, mass spectroscopy, fluorescence detection, ion sensor, light detector or other signal detector.

In some embodiments, it is contemplated that rolling circle amplification products that are sequenced have not been generated based on padlock probes that were ligated after hybridization to PCR products. In specific embodiments, sequencing of rolling circle amplification products depends on replication of padlock probes that hybridize to cDNA that is complementary to an RNA transcript in a sample.

As will be appreciated by the skilled person, the present method may be used in various diagnostic applications, in particular those that require single nucleotide sensitivity. For example, this method may be used to detect point mutations which are associated with disease, disease risk or predisposition, or with responsiveness to treatment, etc., e.g. activating mutations in oncogenes.

Methods may be adapted for automation, for example, by applying procedures as used in conventional automated FISH assays. In certain embodiments, the solutions used for performing one or more reactions may be important for efficiency and the integrity of the detection methods. In some embodiments, an effort to decrease evaporation/dryback during periods of prolonged incubation at elevated temperatures.

The viscosity is the tendency of the fluid to resist flow. Increasing the concentration of a dissolved or dispersed substance generally gives rise to increasing viscosity (i.e., thickening), as does increasing the molecular weight of a solute (a dissolved substance).

The relationship between viscosity and concentration is generally linear up to viscosity values of about twice that of water. This dependency means that more extended molecules (e.g., linear polymers) increase the viscosity to greater extents at low concentrations than more compact molecules (e.g., highly branched polymers) of similar molecular weight.

The following substances may be added to increase viscosity of solutions: alcohols or polyols such as glycerol or glycerine, ethylene glycol or 1,2-ethanediol, poly ethylene glycol (PEG) (an oligomer or polymer of ethylene oxide), diethylene glycol (DEG), or PVA or polyvinyl alcohol (synthetic polymer); saccharides or proteins such as trehalose (naturally occurring disaccharide,) glucose, fructose, dextran sulphate (sulphated polysaccharide), betaine or N,N,N-trimethylglycine (N-trimethylated amino acid); natural hydrocolloids such as botanical, animal and microbial hydrocolloids that include but are not limited to acacia gum (gum Arabic, which is a mixture of polysaccharides and glycoproteins, derived from tree bark), tragacanth (mixture of polysaccharides, derived from shrubs), guar gum (polysaccharide, derived from seed of shrubs), locust bean gum (polysaccharide, derived from seeds), agarose (linear polysaccharide, derived from seaweed), agar (mixture of agarose (linear polysaccharide) and agaropectin, derived from seaweed), carageenan (linear sulfated polysaccharide, derived from seaweed), alginate (anionic polysaccharide, derived from seaweed), cellulose (polysaccharide), xanthan gum (polysaccharide, microbial origin), pectin (heteropolysaccharide), gelatin (mixture of peptides and proteins, animal origin); semisynthetic hydrocolloids, which are hydrocolloids of natural origin that have been modified by further chemical process, and examples are copolymers of starch or cellulose, such as starch-acrylonitrile graft copolymer (a starch polyacrylate salt, and sulfuric acid), vinyl sulfonate, methacrylic acid, vinyl alcohol, vinyl chloride copolymers, methyl cellulose, (CMC) SodiumCarboxyMethylCellulose, (HMC) HydroxyMethylCellulose, (HEMC) HydroxyEthylMethylCellulose, (HPMC) HydroxyPropylMethylCellulose, (HEC) HydroxyEthylCellulose, and (HPC) HydroxyPropylCellulose; synthetic hydrocolloids such as Carbopol®; surfactants such as Tween (polysorbate), NP-40, Triton X-100, SDS (sodium dodecyl sulphate), pluronics/poloxamers, which block copolymers based on ethylene oxide and propylene oxide; miscellaneous polymers such as polyvinyl pyrrolidone (PVP) (polymer made from the monomer N-vinylpyrrolidone) and carbomers (synthetic high molecular weight polymers of acrylic acid), ammonium salts such as tetramethylammonium chloride (TMAC) or other quaternary ammonium salt; amides such as formamide, n-methylformamide, dimethylformamide, 2-pyrollidone, methylpyrollidone, hydroxyethylpyrollidone, acetamide, methylacetamide, dimethylacetamide, propionamide, isobutyramide; organosulfur compounds such as DMSO; amino alcohols or glycols or polyols such as aminoglycols, aminopolyols, 3-amino-1,2-propandiol, diethanolamine, or triethanolamine; organic borates such as 1-butyl-4methylpyridium tetrafluoroborate; organic sulfates such as 1-butyl-3methylimidazolium 2 ethyl sulphate; organic phosphates; or, clays such as Benonite or Veegum®. Other examples of hydrocolloid compositions include those in U.S. Patent Publication 2009/0317467, which is hereby incorporated by reference.

Other patents discuss viscosity enhancers such as U.S. Pat. No. 5,405,741, which is hereby incorporated by reference. It describes that suitable organic solvent diluents include, for example, alcohols such as methanol, ethanol, isopropanol, butanol, sec-butyl alcohol, and the like; ethers such as dimethyl ether, ethyl methyl ether, diethyl ether, 1-ethoxypropane, and the like; tetrahydrofuran; glycols such as 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol, and the like; ketones such as acetone, methylethylketone, 3-pentanone, methylisobutylketone, and the like; esters such as ethyl formate, methyl acetate, ethyl acetate, butyl acetate, ethyl propionate, b-ethoxyethylacetate, methyl Cellosolve acetate, and the like; amides such as formamide, acetamide, succinic amide, and the like; alkyl esters of a suitable acid such as phthalic acid, including methyl phthalate, ethyl phthalate, propyl phthalate, n-butyl phthalate, di-n-butyl phthalate, n-amyl phthalate, isoamyl phthalate, dioctyl phthalate and the like; alkyl amides such as N,N-diethyllaurylamide and the like; trimellitic acid esters including tri-tertoctyl mellitate and the like; phosphoric acid esters including polyphenyl phosphate, tricresyl phosphate, dioctylbutyl phosphate and the like; citric acid esters such as acetyl tributyl citrate and the like; and mixtures thereof. In some embodiments there are aqueous compositions containing at least about 80% by weight of water, at least about 90, or up to about 20% by weight of the composition of an organic solvent, or a maximum of about 10%. In some embodiments, aqueous compositions are free of organic solvent. Suitable hydrophilic colloidal materials include both naturally occurring substances such as proteins, protein derivatives, cellulose derivatives such as cellulose esters; gelatin including alkali-treated and acid-treated gelatin, phthalated gelatin, and the like; polysaccharides such as dextran, gum arabic, zein, casein, pectin, collagen derivatives, collodion, agar-agar, arrowroot, albumin and the like. Generally, it is preferred that the aqueous gelatin composition contains at least about 2% by weight of the composition of gelatin; most preferred are aqueous gelatin compositions in which a gelatin is the hydrophilic colloid. Other hydrophilic colloidal materials that can be used include poly(vinyllactams), acrylamide polymers, polyvinyl alcohol and its derivatives, polyvinyl acetals, polymers of alkyl and sulfoalkyl acrylates and methacrylates, hydrolyzed polyvinyl acetates, polyamides, polyvinyl pyridine, acrylic acid polymers, maleic anhydride copolymers, polyalkylene oxides, methacrylamide copolymers, polyvinyl oxazolidinones, maleic acid copolymers, vinylamine copolymers, methacrylic acid copolymers, acryloyloxyalkylsulfonic acid copolymers, sulfoalkylacrylamide copolymers, polyalkyleneimine copolymers, polyamines, N,N-dialkylaminoalkyl acrylates, vinyl imidazole copolymers, vinyl sulfide copolymers, halogenated styrene polymers, amineacrylamide polymers, polypeptides and the like. Other exemplary colloids are disclosed, for example in U.S. Pat. Nos. 2,691,582; 2,787,545; 2,956,880; 3,132,945; 3,138,846; 3,679,425; 3,706,564; 3,813,251; 3,852,073; 3,879,205; 3,003,879; 3,284,207; 3,748,143; 3,536,491 and the like, the disclosures of which are hereby incorporated herein by reference. A copolymer of any suitable alkali metal or ammonium salt of a sulfonic acid containing monomer with any suitable unsaturated monomer, preferably having a number average molecular weight greater than about 300,000, can be used as the viscosity enhancing agent or thickener. Any suitable method can be used to prepare the viscosity enhancing polymers as is known in the art. For example, any suitable base can be reacted with any suitable ester to form the alkali metal or ammonium salt of the sulfonic acid containing copolymer including acryloyl-oxymethyl bisulfite, acryloyloxymethyl bisulfate, methacryloyloxymethyl bisulfite, methacryloyloxymethyl bisulfate, acryloyloxyethyl bisulfite, acryloyloxyethyl bisulfate, methacryloyloxyethyl bisulfite, methacryloyloxyethyl bisul-fate, acryloyloxypropyl bisulfite, acryloyloxypropyl bisul-fate, methacryloyloxypropyl bisulfite, methacryloyloxypropyl bisulfate, acryloyloxybutyl bisulfite, acryloyloxybutyl bisulfate, methacryloyloxybutyl bisulfite methacryloylxybutyl bisulfate, and the like. The corresponding salt that is reacted with an unsaturated monomer to prepare one or more copolymers can be obtained by reacting the ester with a base as is well known.

It will be understood by a person of ordinary skill in the art that methods may involve a number of steps, some of which may be repeated throughout a protocol. It is contemplated that one or more of these steps may be repeated, be repeated at least, or be repeated at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 time or more (or any range derivable therein). In some embodiments, methods involve or involve at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the following additional steps (above the rolling circle amplification steps) in the same or a similar order to achieve detection, identification or characterization of a nucleic acid sequence in a biological sample, including one that has been prepared for analysis on a slide:

-   -   1) dewaxing, such as to remove wax from tissue;     -   2) alcohol rinsing, such as to remove dewaxing reagents and/or         hydrate sample;     -   3) washing the sample,     -   4) heating the sample, such as to induce epitope retrieval         (HIER);     -   5) washing the sample;     -   6) incubating with a peroxidase block, such as hydrogen peroxide         or methanol to reduce or eliminate endogenous peroxidase         activity in a sample     -   7) washing the sample;     -   8) incubating with an antibody or antibody fragment under         conditions to allow the antibody or antibody fragment to bind a         label on a detection probe;     -   9) washing the sample;     -   10) incubating the sample with a secondary antibody that binds         any antibody or antibody fragment that binds to a label on a         detection probe;     -   11) washing the sample     -   12) detecting any label on the secondary antibody

In particular embodiments, instead of employing an antibody in step 8), a reagent that reacts with a detection probe label is incubated under conditions to detect the label. For instance, in some embodiments, a detection probe is labeled with horse radish peroxidase (HRP) (such as by conjugation), and detection of the label is achieved by incubating the sample with a reagent that allows detection of the label, such as 3,3′-diaminobenzidine tetrahydrochloride (DAB). In other embodiments, a detection probe may be labeled with alkaline phosphatase (AP), which may be detected directly or indirectly (such as with an antibody, that may or may not be labeled but is capable of detection).

In certain embodiments, all of these steps are employed. A sample may be heated at one or multiple times during a process. Heating a sample may be employed to inactivate one or more enzyme or reagents. In other embodiments, heating is used prior to immunohistochemistry (IHC) or in situ hybridization (ISH) to improve staining. Embodiments involve heating a sample to about, at least about, or at most about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, or 125° C. (and any range derivable therein) for about, at least about, or at most about 30 seconds, 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 minutes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 hours (and any range derivable therein). A person of ordinary skill in the art will know how temperatures and times may be varied depending on factors that include but are not limited to the sample, volume of the sample and volume of liquid, surface area, reagents present, target of the heating, pH, etc. It is contemplated that in some embodiments, one or more additional enzymes may be employed in conjunction with heating, such as to inactivate one or more enzymes the sample or to make a sample more accessible. In some embodiments, an enzyme that reduces or minimizes protein crosslinking in the sample is employed.

E. KRAS

As described in more detail herein, methods may be used to detect a point mutation in the mRNA sequence that codes for KRAS. KRAS is one of the most frequently activated oncogenes. As used herein, “KRAS” refers to v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog. KRAS is also known in the art as NS3, KRAS1, KRAS2, RASK2, KI-RAS, C-K-RAS, K-RAS2A, K-RAS2B, K-RAS4A and K-RAS4B. This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution can be responsible for an activating mutation. The transforming protein that results can be implicated in various malignancies, including lung cancer, colon cancer, thyroid cancer and pancreatic cancer and is strongly associated with resistance to epidermal growth factor receptor (EGFR) inhibitor therapy. For example, in metastatic colorectal cancer the presence of mutations in the KRAS gene is routinely analyzed, and a positive mutation status indicates that the tumor will not respond to EGFR antibody therapy. In lung adenocarcinoma KRAS mutations are associated with smoking, poor prognosis and non-responsiveness to EGFR tyrosine kinase inhibitors (TKI) whereas KRAS wild-type tumors with EGFR mutations are linked to non-smoking, better prognosis and response to EGFR-TKI therapy.

A tumor may have one or more mutations in KRAS (e.g., an activating mutation), unwanted expression of KRAS (e.g., overexpression over wild type), KRAS deficiency, and/or amplification of KRAS gene (e.g., having more than two functional copies of KRAS gene). There are seven point mutations in codon 12 and 13 that together account for more than 95% of all KRAS mutations. Conventional KRAS analysis is based on DNA extracted from crude tumor tissue, and after PCR amplification of the hot spot region on exon 1 the sequence aberrations in codon 12 and 13 are characterized by direct dideoxy sequencing or by more sensitive targeted assays such as Pyrosequencing or allele-specific PCR. Thus, all different cell types present in a tumor sample—normal parenchymal cells, stromal cells, inflammatory cells, different pre-neoplastic and neoplastic sub-clones—contribute their wild-type and mutated KRAS alleles to these assays. In the routine diagnostic setting tumor cells can be enriched for by manual microdissection, but in order to annotate a mutation to a certain tumor sub compartment the required dissection is laborious. Still, single cell resolution is extremely difficult to achieve. This might not be a problem in colorectal cancer as activating KRAS mutations are considered to be early events in tumorigenesis and presumably homogenously distributed in the tumor. However, for other types of cancer, and for mutations in other oncogenes, very little is known about heterogeneity among cancer sub-clones and its impact on tumor biology and treatment response. Therefore, methods which offer genotyping directly on tissue sections are highly warranted. Hence there is a requirement for sensitive KRAS mutation analysis to determine the most suitable treatment for the patients.

As described herein the present method may be used in a genotyping assay that targets KRAS-mutations in codon 12 and 13 in situ on tissue samples by the use of multiple mutation specific padlock probes and rolling-circle amplification. Such an in situ technique offers single transcript analysis directly in tissues and thus circumvents traditional DNA extraction from heterogeneous tumor tissues. In addition, or alternatively, mutations in codon 61 and/or codon 146 of KRAS may be targeted (for specific information see also Loupakis et al., 2009, Br J Cancer, 101(4): 715-21, which is incorporated herein by reference in its entirety). Furthermore, mutations in the 3′ UTR of KRAS transcripts may be targeted (for specific information see also Graziano et al., 2010, Pharmacogenomics J., doi 10.1038/tpj.2010.9, which is incorporated herein by reference in its entirety). These mutations may be detected in combination with a detection of codon 12, 13, 61 and/or 146 mutations, or they may be detected alone, or in combination with codon 12 mutations, or with codon 13 mutations, or with codon 61 mutations, or with codon 146 mutation, or with any subgrouping of codon 12, 13, 61 and 146 mutations. Methods may be carried out in fresh frozen or formalin-fixed, paraffin-embedded (FFPE) tissue, or in tissues in touch imprint samples. In some embodiments, tissue samples may be cancer tissue, e.g. colon or lung tissues.

In some embodiments, methods and compositions concern KRAS mutations, particularly those mutations that have been found in cancer cells. The term “KRAS mutation associated with cancer” or “KRAS mutant associated with tumor development” refers to a mutation in the KRAS gene or a corresponding mutant, that has been identified in the Sanger database as of Feb. 15, 2012 as associated with cancer or precancer (on the world wide web at sanger.ac.uk). In certain embodiments, the methods and compositions concern detecting a plurality of mutations. In some embodiments a plurality of mutations refers to at least or at most the following percentage of mutations in that gene associated with cancer: 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or 100%, or any range derivable therein.

F. EGFR

The epidermal growth factor receptor (EGFR) is an important target in the treatment of some cancers. The combination of anti-EGFR antibodies with chemotherapy is thus commonly used in the treatment of these cancers. The KRAS protein is an important mediator in the signal transduction cascade regulated by the EGFR. Mutations in the KRAS gene are a very important factor in the selection of molecular biological treatment options targeted against EGFR. Studies have shown that if the mutation is present, anti-EGFR medications such as cetuximab (Erbitux) and panitumumab (Vectibix) are not sufficiently effective to warrant their use. Thus, as discussed herein, the present method may advantageously be used to detect the presence or absence of a point mutation in the mRNA which codes for KRAS, wherein the identification of KRAS wild-type mRNA indicates that the cancer may be treated with EGFR inhibitors.

In addition, the present method may be used to detect the presence or absence of a mutation in the mRNA which codes for the EGFR. Examples of EGFR mutations that may be detected according to various embodiments are shown in Table 7.

G. Braf, APC, PTEN, PI3K

Methods may be further used to detect one or more point mutations in the mRNA sequence that codes for Braf, APC, PTEN or PI3K. Suitable Braf mutations are known to the skilled person and are described in Rajagopalan et al., 2002, Nature, 418 (29), 934 and Monticone et al., 2008, Molecular Cancer, 7(92), which are incorporated herein by reference in their entirety. Particularly preferred is the detection of mutation V600E. In some embodiments, methods further involve the detection of one or more point mutations in KRAS and Braf. Braf and KRAS mutations are described as being mutually exclusive regarding the function of downstream pathway elements. Thus, by determining mutations in Braf and KRAS at the same time, it may be elucidate whether and pathway functions are compromised by genetic mutations.

Suitable APC mutations are known to the skilled person and are described, for example, in Vogelstein and Fearon, 1988, N Engl J Med, 319(9): 525-32, which is incorporated herein by reference in its entirety.

Suitable PTEN mutations are known to the skilled person and are described, for example, in Laurent-Puig et al, 2009, J Clon Oncol, 27(35), 5924-30 or Loupakis et al., 2009, J clin Oncol, 27(16), 2622-9, which are incorporated herein by reference in their entirety.

Suitable PI3K mutations are known to the skilled person and are described, for example, in Satore-Bianchi et al., 2009, Cancer Res., 69(5), 1851-7 or Prenen et al., 2009, Clin Cancer Res., 15(9), 3184-8, which are incorporated herein by reference in their entirety.

In some embodiments, methods and compositions concern Braf, APC, PTEN or PI3K mutations. In further embodiments, methods and compositions concern KRAS mutations in combination with Braf mutations, and/or in combination with APC mutations, and/or in combination with PTEN mutations, and/or in combination with PI3K mutations, particularly those mutations that have been found in cancer cells. Such mutations may be derived from suitable literature sources, e.g. those mentioned above, or may be identified according to suitable databases, e.g., the Sanger database as of Feb. 15, 2012 (on the world wide web at sanger.ac.uk). In certain embodiments, the methods and compositions concern detecting a plurality of the mutations. In some embodiments a plurality of mutations refers to at least or at most the following percentage of mutations in that the gene or gene combination associated with cancer: 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or 100%, or any range derivable therein.

Other embodiments concern characterization, detection, sequencing, and/or analyzing one or more cancer genes shown below. In certain embodiments, there is one or more padlock probes with arms that flank a cancer mutation. In further embodiments, there is one or more padlock probes with the arms discussed above and a sequence(s) at the terminal end of one of the arms that is complementary or identical to a mutation sequence (whether the mutation is a single nucleotide chain or a mutation involving a deletion, insertion, alteration of multiple nucleotides).

TABLE B Tumor Types Chr (Somatic Cancer Tissue Mutation Symbol Name Gene ID Band Mutations) Syndrome Type* Type* ABL1 v-abl Abelson murine 25 9q34.1 CML, ALL, T- L T, Mis leukemia viral ALL oncogene homolog 1 ABL2 v-abl Abelson murine 27 1q24-q25 AML L T leukemia viral oncogene homolog 2 ACSL3 acyl-CoA synthetase 2181 2q36 prostate E T long-chain family member 3 AF15Q14 AF15q14 protein 57082 15q14 AML L T AF1Q ALL1-fused gene from 10962 1q21 ALL L T chromosome 1q AF3p21 SH3 protein interacting 51517 3p21 ALL L T with Nck, 90 kDa (ALL1 fused gene from 3p21) AF5q31 ALL1 fused gene from 27125 5q31 ALL L T 5q31 AKAP9 A kinase (PRKA) 10142 7q21-q22 papillary thyroid E T anchor protein (yotiao) 9 AKT1 v-akt murine thymoma 207 14q32.32 breast, E Mis viral oncogene colorectal, homolog 1 ovarian, NSCLC AKT2 v-akt murine thymoma 208 19q13.1-q13.2 ovarian, E A viral oncogene pancreatic homolog 2 ALDH2 aldehyde 217 12q24.2 leiomyoma M T dehydrogenase 2 family (mitochondrial) ALK anaplastic lymphoma 238 2p23 ALCL, NSCLC, Familial L, E, M T, Mis, A kinase (Ki-1) Neuroblastoma neuroblastoma ALO17 KIAA1618 protein 57714 17q25.3 ALCL L T APC adenomatous 324 5q21 colorectal, Adenomatous E, M, O D, Mis, N, polyposis of the colon pancreatic, polyposis F, S gene desmoid, coli; Turcot hepatoblastoma syndrome glioma, other CNS ARHGEF12 RHO guanine 23365 11q23.3 AML L T nucleotide exchange factor (GEF) 12 (LARG) ARHH RAS homolog gene 399 4p13 NHL L T family, member H (TTF) ARID1A AT rich interactive 8289 1p35.3 clear cell E Mis, N, F, domain 1A (SWI-like) ovarian S, D carcinoma, RCC ARID2 AT rich interactive 196528 12q12 hepatocellular E N, S, F domain 2 carcinoma ARNT aryl hydrocarbon 405 1q21 AML L T receptor nuclear translocator ASPSCR1 alveolar soft part 79058 17q25 alveolar soft M T sarcoma chromosome part sarcoma region, candidate 1 ASXL1 additional sex combs 171023 20q11.1 MDS, CMML L F, N, Mis like 1 ATF1 activating transcription 466 12q13 malignant E, M T factor 1 melanoma of soft parts, angiomatoid fibrous histiocytoma ATIC 5-aminoimidazole-4- 471 2q35 ALCL L T carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase ATM ataxia telangiectasia 472 11q22.3 T-PLL Ataxia- L, O D, Mis, N, mutated telangiectasia F, S ATRX alpha 546 Xq21.1 Pancreatic E Mis, F, N thalassemia/mental neuroendocrine retardation syndrome tumors, X-linked paediatric GBM BAP1 BRCA1 associated 8314 3p21.31-p21.2 uveal E N, Mis, F, protein-1 (ubiquitin melanoma, S, O carboxy-terminal breast, NSCLC, hydrolase) RCC BCL10 B-cell CLL/lymphoma 8915 1p22 MALT L T 10 BCL11A B-cell CLL/lymphoma 53335 2p13 B-CLL L T 11A BCL11B B-cell CLL/lymphoma 64919 14q32.1 T-ALL L T 11B (CTIP2) BCL2 B-cell CLL/lymphoma 2 596 18q21.3 NHL, CLL L T BCL3 B-cell CLL/lymphoma 3 602 19q13 CLL L T BCL5 B-cell CLL/lymphoma 5 603 17q22 CLL L T BCL6 B-cell CLL/lymphoma 6 604 3q27 NHL, CLL L T, Mis BCL7A B-cell CLL/lymphoma 605 12q24.1 BNHL L T 7A BCL9 B-cell CLL/lymphoma 9 607 1q21 B-ALL L T BCOR BCL6 corepressor 54880 Xp11.4 retinoblastoma, F, N, S, T AML, APL(translocation) BCR breakpoint cluster 613 22q11.21 CML, ALL, AML L T region BHD folliculin, Birt-Hogg- 201163 17p11.2 Birt-Hogg- E, M Mis. N, F Dube syndrome Dube syndrome BIRC3 baculoviral IAP repeat- 330 11q22-q23 MALT L T containing 3 BLM Bloom Syndrome 641 15q26.1 Bloom L, E Mis, N, F Syndrome BMPR1A bone morphogenetic 657 10q22.3 Juvenile E Mis, N, F protein receptor, type polyposis IA BRAF v-raf murine sarcoma 673 7q34 melanoma, E Mis, T, O viral oncogene colorectal, homolog B1 papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma BRCA1 familial breast/ovarian 672 17q21 ovarian Hereditary E D, Mis, N, cancer gene 1 breast/ovarian F, S cancer BRCA2 familial breast/ovarian 675 13q12 breast, ovarian, Hereditary L, E D, Mis, N, cancer gene 2 pancreatic breast/ovarian F, S cancer BRD3 bromodomain 8019 9q34 lethal midline E T containing 3 carcinoma of young people BRD4 bromodomain 23476 19p13.1 lethal midline E T containing 4 carcinoma of young people BRIP1 BRCA1 interacting 83990 17q22 Fanconi L, E F, N, Mis protein C-terminal anaemia J, helicase 1 breast cancer susceptiblity BTG1 B-cell translocation 694 12q22 BCLL L T gene 1, anti- proliferative BUB1B BUB1 budding 701 15q15 Mosaic M Mis, N, F, S uninhibited by variegated benzimidazoles 1 aneuploidy homolog beta (yeast) C12orf9 chromosome 12 open 93669 12q14.3 lipoma M T reading frame 9 C15orf21 chromosome 15 open 283651 15q21.1 prostate E T reading frame 21 C15orf55 chromosome 15 open 256646 15q14 lethal midline E T reading frame 55 carcinoma C16orf75 chromosome 16 open 116028 16p13.13 PMBL, Hodgkin L T reading frame 75 Lymphona, C2orf44 chromosome 2 open 80304 2p23.3 NSCLC E T reading frame 44 CAMTA1 calmodulin binding 611501 1p36.31-p36.23 epitheliod M T transcription activator 1 hemangioendot helioma CANT1 calcium activated 124583 17q25 prostate E T nucleotidase 1 CARD11 caspase recruitment 84433 7p22 DLBCL L Mis domain family, member 11 CARS cysteinyl-tRNA 833 11p15.5 ALCL L T synthetase CBFA2T1 core-binding factor, 862 8q22 AML L T runt domain, alpha subunit 2; translocated to, 1 (ETO) CBFA2T3 core-binding factor, 863 16q24 AML L T runt domain, alpha subunit 2; translocated to, 3 (MTG-16) CBFB core-binding factor, 865 16q22 AML L T beta subunit CBL Cas-Br-M (murine) 867 11q23.3 AML, JMML, L T, Mis S, O ecotropic retroviral MDS transforming CBLB Cas-Br-M (murine) 868 3q13.11 AML L Mis S ecotropic retroviral transforming sequence b CBLC Cas-Br-M (murine) 23624 19q13.2 AML L M ecotropic retroviral transforming sequence c CCDC6 coiled-coil domain 8030 10q21 NSCLC E T containing 6 CCNB1IP1 cyclin B1 interacting 57820 14q11.2 leiomyoma M T protein 1, E3 ubiquitin protein ligase CCND1 cyclin D1 595 11q13 CLL, B-ALL, L, E T breast CCND2 cyclin D2 894 12p13 NHL, CLL L T CCND3 cyclin D3 896 6p21 MM L T CCNE1 cyclin E1 898 19q12 serous ovarian E A CD273 programmed cell death 80380 9p24.2 PMBL, Hodgkin L T 1 ligand 2 Lymphona, CD274 CD274 molecule 29126 9p24 PMBL, Hodgkin L T Lymphona, CD74 CD74 molecule, major 972 5q32 NSCLC E T histocompatibility complex, class II invariant chain CD79A CD79a molecule, 973 19q13.2 DLBCL L O, S immunoglobulin- associated alpha CD79B CD79b molecule, 974 17q23 DLBCL L Mis, O immunoglobulin- associated beta CDH1 cadherin 1, type 1, E- 999 16q22.1 lobular breast, Familial E Mis, N, F, S cadherin (epithelial) gastric gastric (ECAD) carcinoma CDH11 cadherin 11, type 2, 1009 16q22.1 aneurysmal M T OB-cadherin bone cysts (osteoblast) CDK12 cyclin-dependent 51755 17q12 serous ovarian E Mis, N, F kinase 12 CDK4 cyclin-dependent 1019 12q14 Familial E Mis kinase 4 malignant melanoma CDK6 cyclin-dependent 1021 7q21-q22 ALL L T kinase 6 CDKN2A cyclin-dependent 1029 9p21 melanoma, Familial L, E, D, Mis, N, kinase inhibitor 2A multiple other malignant M, O F, S (p16(INK4a)) gene tumour types melanoma CDKN2a cyclin-dependent 1029 9p21 melanoma, Familial L, E, D, S (p14) kinase inhibitor 2A-- multiple other malignant M, O p14ARF protein tumour types melanoma CDKN2C cyclin-dependent 1031 1p32 glioma, MM O, L D kinase inhibitor 2C (p18, inhibits CDK4) CDX2 caudal type homeo 1045 13q12.3 AML L T box transcription factor 2 CEBPA CCAAT/enhancer 1050 19q13.1 AML, MDS L Mis, N, F binding protein (C/EBP), alpha CEP1 centrosomal protein 1 11064 9q33 MPD, NHL L T CHCHD7 coiled-coil-helix-coiled- 79145 8q11.2 salivary E T coil-helix domain adenoma containing 7 CHEK2 CHK2 checkpoint 11200 22q12.1 familial E F homolog (S. pombe) breast cancer CHIC2 cysteine-rich 26511 4q11-q12 AML L T hydrophobic domain 2 CHN1 chimerin (chimaerin) 1 1123 2q31-q32.1 extraskeletal M T myxoid chondrosarcoma CIC capicua homolog 23152 19q13.2 oligodendroglioma O Mis, F, S CIITA class II, major 4261 16p13 PMBL, Hodgkin L T histocompatibility Lymphona, complex, transactivator CLTC clathrin, heavy 1213 17q11-qter ALCL, renal L T polypeptide (Hc) CLTCL1 clathrin, heavy 8218 22q11.21 ALCL L T polypeptide-like 1 CMKOR1 chemokine orphan 57007 2q37.3 lipoma M T receptor 1 COL1A1 collagen, type I, alpha 1 1277 17q21.31-q22 dermatofibrosarcoma M T protuberans, aneurysmal bone cyst COPEB core promoter element 1316 10p15 prostate, glioma E, O Mis, N binding protein (KLF6) COX6C cytochrome c oxidase 1345 8q22-q23 uterine M T subunit VIc leiomyoma CREB1 cAMP responsive 1385 2q34 clear cell M T element binding sarcoma, protein 1 angiomatoid fibrous histiocytoma CREB3L1 cAMP responsive 90993 11p11.2 myxofibrosarcoma M T element binding protein 3-like 1 CREB3L2 cAMP responsive 64764 7q34 fibromyxoid M T element binding sarcoma protein 3-like 2 CREBBP CREB binding protein 1387 16p13.3 ALL, AML, L T, N, F, (CBP) DLBCL, B-NHL Mis, O CRLF2 cytokine receptor-like 64109 Xp22.3; B-ALL, Downs L Mis, T factor 2 Yp11.3 associated ALL CRTC3 CREB regulated 64784 15q26.1 salivary gland E T transcription mucoepidermoid coactivator 3 CTNNB1 catenin (cadherin- 1499 3p22-p21.3 colorectal, E, M, O H, Mis, T associated protein), cvarian, beta 1 hepatoblastoma, others, pleomorphic salivary adenoma CYLD familial cylindromatosis 1540 16q12-q13 cylindroma Familial E Mis, N, F, S gene cylindromatosis D10S170 DNA segment on 8030 10q21 papillary thyroid, E T chromosome 10 CML (unique) 170, H4 gene (PTC1) DAXX death-domain 1616 6p21.3 Pancreatic E Mis, F, N associated protein neuroendocrine tumors. Paediatric GBM DDB2 damage-specific DNA 1643 11p12 Xeroderma E Mis, N binding protein 2 pigmentosum (E) DDIT3 DNA-damage- 1649 12q13.1-q13.2 liposarcoma M T inducible transcript 3 DDX10 DEAD (Asp-Glu-Ala- 1662 11q22-q23 AML* L T Asp) box polypeptide 10 DDX5 DEAD (Asp-Glu-Ala- 1655 17q21 prostate E T Asp) box polypeptide 5 DDX6 DEAD (Asp-Glu-Ala- 1656 11q23.3 B-NHL L T Asp) box polypeptide 6 DEK DEK oncogene (DNA 7913 6p23 AML L T binding) DICER1 dicer 1, ribonuclease 23405 14q32.13 sex cordstromal Familial E, M, O Mis F, N type III tumour, Pleuropulmonary TGCT, Blastoma embryonal rhadomyosarcoma DNM2 dynamin 2 1785 19p13.2 ETP ALL L F, N, Splice, Mis, O DNMT3A DNA (cytosine-5-)- 1788 2p23 AML L Mis, F, N, S methyltransferase 3 alpha DUX4 double homeobox, 4 22947 4q35 soft tissue M T sarcoma EBF1 early B-cell factor 1 1879 5q34 lipoma M T ECT2L epithelial cell 345930 6q24.1 ETP ALL L N, Splice, transforming sequence Mis 2 oncogene-like EGFR epidermal growth 1956 7p12.3-p12.1 glioma, NSCLC Familial lung E, O A, O, Mis factor receptor cancer (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) EIF4A2 eukaryotic translation 1974 3q27.3 NHL L T initiation factor 4A, isoform 2 ELF4 E74-like factor 4 (ets 2000 Xq26 AML L T domain transcription factor) ELK4 ELK4, ETS-domain 2005 1q32 prostate E T protein (SRF accessory protein 1) ELKS ELKS protein 23085 12p13.3 papillary thyroid E T ELL ELL gene (11-19 8178 19p13.1 AL L T lysine-rich leukemia gene) ELN elastin 2006 7q11.23 B-ALL L T EML4 echinoderm 27436 2p21 NSCLC E T microtubule associated protein like 4 EP300 300 kd E1A-Binding 2033 22q13 colorectal, L, E T, N, F, protein gene breast, Mis, O pancreatic, AML, ALL, DLBCL EPS15 epidermal growth 2060 1p32 ALL L T factor receptor pathway substrate 15 (AF1p) ERBB2 v-erb-b2 erythroblastic 2064 17q21.1 breast, ovarian, E A, Mis, O leukemia viral other tumour oncogene homolog 2, types, NSCLC, neuro/glioblastoma gastric derived oncogene homolog (avian) ERCC2 excision repair cross- 2068 19q13.2-q13.3 Xeroderma E Mis, N, F, S complementing rodent pigmentosum repair deficiency, (D) complementation group 2 (xeroderma pigmentosum D) ERCC3 excision repair cross- 2071 2q21 Xeroderma E Mis, S complementing rodent pigmentosum repair deficiency, (B) complementation group 3 (xeroderma pigmentosum group B complementing) ERCC4 excision repair cross- 2072 16p13.3-p13.13 Xeroderma E Mis, N, F complementing rodent pigmentosum repair deficiency, (F) complementation group 4 ERCC5 excision repair cross- 2073 13q33 Xeroderma E Mis, N, F complementing rodent pigmentosum repair deficiency, (G) complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) ERG v-ets erythroblastosis 2078 21q22.3 Ewing sarcoma, M, E, L T virus E26 oncogene prostate, AML like (avian) ETV1 ets variant gene 1 2115 7p22 Ewing sarcoma, M, E T prostate ETV4 ets variant gene 4 2118 17q21 Ewing sarcoma, M, E T (E1A enhancer binding Prostate protein, E1AF) carcinoma ETV5 ets variant gene 5 2119 3q28 Prostate E T ETV6 ets variant gene 6 2120 12p13 congenital L, E, M T (TEL oncogene) fibrosarcoma, multiple leukemia and lymphoma, secretory breast, MDS, ALL EVI1 ecotropic viral 2122 3q26 AML, CML L T integration site 1 EWSR1 Ewing sarcoma 2130 22q12 Ewing sarcoma, L, M T breakpoint region 1 desmoplastic (EWS) small round cell tumor, ALL, clear cell sarcoma, sarcoma, myoepithelioma EXT1 multiple exostoses 2131 8q24.11-q24.13 Multiple M Mis, N, F, S type 1 gene Exostoses Type 1 EXT2 multiple exostoses 2132 11p12-p11 Multiple M Mis, N, F, S type 2 gene Exostoses Type 2 EZH2 enhancer of zeste 2146 7q35-q36 DLBCL L Mis homolog 2 EZR ezrin 7430 6q25.3 NSCLC E T FACL6 fatty-acid-coenzyme A 23305 5q31 AML, AEL L T ligase, long-chain 6 FAM22A family with sequence 728118 10q23.2 edometrial M T similarity 22, member A stromal sarcoma FAM22B family with sequence 729262 10q22.3 edometrial M T similarity 22, member B stromal sarcoma FAM46C family with sequence 54855 1p12 MM L Mis, F, O similarity 46, member C FANCA Fanconi anemia, 2175 16q24.3 Fanconi L D, Mis, N, complementation anaemia A F, S group A FANCC Fanconi anemia, 2176 9q22.3 Fanconi L D, Mis, N, complementation anaemia C F, S group C FANCD2 Fanconi anemia, 2177 3p26 Fanconi L D, Mis, N, F complementation anaemia D2 group D2 FANCE Fanconi anemia, 2178 6p21-p22 Fanconi L N, F, S complementation anaemia E group E FANCF Fanconi anemia, 2188 11p15 Fanconi L N, F complementation anaemia F group F FANCG Fanconi anemia, 2189 9p13 Fanconi L Mis, N, F, S complementation anaemia G group G FBXO11 F-box protein 11 80204 2p16.3 DLBCL L Mis, F, D FBXW7 F-box and WD-40 55294 4q31.3 colorectal, E, L Mis, N, D, F domain protein 7 endometrial, T- (archipelago homolog, ALL Drosophila) FCGR2B Fc fragment of IgG, 2213 1q23 ALL L T low affinity IIb, receptor for (CD32) FEV FEV protein - 54738 2q36 Ewing sarcoma M T (HSRNAFEV) FGFR1 fibroblast growth factor 2260 8p11.2-p11.1 MPD, NHL L T receptor 1 FGFR1OP FGFR1 oncogene 11116 6q27 MPD, NHL L T partner (FOP) FGFR2 fibroblast growth factor 2263 10q26 gastric. NSCLC, E Mis receptor 2 endometrial FGFR3 fibroblast growth factor 2261 4p16.3 bladder, MM, T- L, E Mis, T receptor 3 cell lymphoma FH fumarate hydratase 2271 1q42.1 hereditary E, M Mis, N, F leiomyomatosis and renal cell cancer FHIT fragile histidine triad 2272 3p14.2 pleomorphic E T gene salivary gland adenoma FIP1L1 FIP1 like 1 (S. cerevisiae) 81608 4q12 idiopathic L T hypereosinophilic syndrome FLI1 Friend leukemia virus 2313 11q24 Ewing sarcoma M T integration 1 FLJ27352 BX648577, FLJ27352 145788 15q21.3 PMBL, Hodgkin L T hypothetical Lymphona, LOC145788 FLT3 fms-related tyrosine 2322 13q12 AML, ALL L Mis, O kinase 3 FNBP1 formin binding protein 23048 9q23 AML L T 1 (FBP17) FOXL2 forkhead box L2 668 3q23 granulosa-cell O Mis tumour of the ovary FOXO1A forkhead box O1A 2308 13q14.1 alveolar M T (FKHR) rhabdomyosarcomas FOXO3A forkhead box O3A 2309 6q21 AL L T FOXP1 forkhead box P1 27086 3p14.1 ALL L T FSTL3 follistatin-like 3 10272 19p13 B-CLL L T (secreted glycoprotein) FUBP1 far upstream element 8880 1p13.1 oligodendroglioma O F, N (FUSE) binding protein 1 FUS fusion, derived from 2521 16p11.2 liposarcoma, M, L T t(12; 16) malignant AML, Ewing liposarcoma sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma FVT1 follicular lymphoma 2531 18q21.3 B-NHL L T variant translocation 1 GAS7 growth arrest-specific 7 8522 17p AML* L T GATA1 GATA binding protein 2623 Xp11.23 megakaryoblastic L Mis, F 1 (globin transcription leukemia of factor 1) Downs Syndrome GATA2 GATA binding protein 2 2624 3q21.3 AML(CML blast L Mis transformation) GATA3 GATA binding protein 3 2625 10p15 breast E F, N, S GMPS guanine 8833 3q24 AML L T monphosphate synthetase GNA11 guanine nucleotide 2767 19p13.3 uveal melanoma E Mis binding protein (G protein), alpha 11 (Gq class) GNAQ guanine nucleotide 2776 9q21 uveal melanoma E Mis binding protein (G protein), q polypeptide GNAS guanine nucleotide 2778 20q13.2 pituitary E Mis binding protein (G adenoma protein), alpha stimulating activity polypeptide 1 GOLGA5 golgi autoantigen, 9950 14q papillary thyroid E T golgin subfamily a, 5 (PTC5) GOPC golgi associated PDZ 57120 6q21 glioblastoma O O and coiled-coil motif containing GPC3 glypican 3 2719 Xq26.1 Simpson- O T, D, Mis, Golabi- N, F, S Behmel syndrome GPHN gephyrin (GPH) 10243 14q24 AL L T GRAF GTPase regulator 23092 5q31 AML, MDS L T, F, S associated with focal adhesion kinase pp125(FAK) H3F3A H3 histone, family 3A 3020 1q42.12 glioma O Mis HCMOGT-1 sperm antigen 92521 17p11.2 JMML L T HCMOGT-1 HEAB ATP_GTP binding 10978 11q12 AML L T protein HERPUD1 homocysteine- 9709 16q12.2-q13 prostate E T inducible, endoplasmic reticulum stress- inducible, ubiquitin-like domain member 1 HEY1 hairy/enhancer-of-split 23462 8q21 mesenchymal M T related with YRPW chondrosarcoma motif 1 HIP1 huntingtin interacting 3092 7q11.23 CMML L T protein 1 HIST1H4I histone 1, H4i (H4FM) 8294 6p21.3 NHL L T HLF hepatic leukemia factor 3131 17q22 ALL L T HLXB9 homeo box HB9 3110 7q36 AML L T HMGA1 high mobility group AT- 3159 6p21 microfollicular E, M T hook 1 thyroid adenoma, various benign mesenchymal tumors, HMGA2 high mobility group AT- 8091 12q15 lipoma, M T hook 2 (HMGIC) leiomyoma, pleiomorphic salivary gland adenoma HNRNPA2B1 heterogeneous nuclear 3181 7p15 prostate E T ribonucleoprotein A2/B1 HOOK3 hook homolog 3 84376 8p11.21 papillary thyroid E T HOXA11 homeo box A11 3207 7p15-p14.2 CML L T HOXA13 homeo box A13 3209 7p15-p14.2 AML L T HOXA9 homeo box A9 3205 7p15-p14.2 AML* L T HOXC11 homeo box C11 3227 12q13.3 AML L T HOXC13 homeo box C13 3229 12q13.3 AML L T HOXD11 homeo box D11 3237 2q31-q32 AML L T HOXD13 homeo box D13 3239 2q31-q32 AML* L T HRAS v-Ha-ras Harvey rat 3265 11p15.5 infrequent Costello E, L, M Mis sarcoma viral sarcomas, rare syndrome oncogene homolog other types HRPT2 hyperparathyroidism 2 3279 1q21-q31 parathyroid Hyperparathy E, M Mis, N, F adenoma roidism-jaw tumor syndrome HSPCA heat shock 90 kDa 3320 14q32.31 NHL L T protein 1, alpha HSPCB heat shock 90 kDa 3326 6p12 NHL L T protein 1, beta IDH1 isocitrate 3417 2q33.3 gliobastoma O Mis dehydrogenase 1 (NADP+), soluble IDH2 socitrate 3418 15q26.1 GBM M M dehydrogenase 2 (NADP+), mitochondrial IGH@ immunoglobulin heavy 3492 14q32.33 MM, Burkitt L T locus lymphoma, NHL, CLL, B- ALL, MALT, MLCLS IGK@ immunoglobulin kappa 50802 2p12 Burkitt L T locus lymphoma, B- NHL IGL@ immunoglobulin 3535 22q11.1-q11.2 Burkitt L T lambda locus lymphoma IKZF1 IKAROS family zinc 10320 7p12.2 ALL, DLBCL L D, T finger 1 IL2 interleukin 2 3558 4q26-q27 intestinal T-cell L T lymphoma IL21R interleukin 21 receptor 50615 16p11 NHL L T IL6ST interleukin 6 signal 3572 5q11 hepatocellular E O transducer (gp130, ca oncostatin M receptor) IL7R interleukin 7 receptor 146661 5p13 ALL, ETP ALL L Mis, O IRF4 interferon regulatory 3662 6p25-p23 MM L T factor 4 IRTA1 immunoglobulin 83417 1q21 B-NHL L T superfamily receptor translocation associated 1 ITK IL2-inducible T-cell 3702 5q31-q32 peripheral T-cell L T kinase lymphoma JAK1 Janus kinase 1 3716 1p32.3-p31.3 ALL L Mis JAK2 Janus kinase 2 3717 9p24 ALL, AML, L T, Mis, O MPD, CML JAK3 Janus kinase 3 3718 19p13.1 acute L Mis megakaryocytic leukemia, ETP ALL JAZF1 juxtaposed with 221895 7p15.2-p15.1 endometrial M T another zinc finger stromal tumours gene 1 JUN jun oncogene 3725 1p32-p31 sarcoma M A KDM5A lysine (K)-specific 5927 12p11 AML L T demethylase 5A, JARID1A KDM5C lysine (K)-specific 8242 Xp11.22-p11.21 clear cell renal E N, F, S demethylase 5C carcinoma (JARID1C) KDM6A lysine (K)-specific 7403 Xp11.2 renal, E, L D, N, F, S demethylase 6A, UTX oesophageal SCC, MM KDR vascular endothelial 3791 4q11-q12 NSCLC, E Mis growth factor receptor 2 angiosarcoma KIAA1549 KIAA1549 57670 7q34 pilocytic O O astrocytoma KIF5B kinesin family member 3799 10p11.22 NSCLC E T 5B KIT v-kit Hardy-Zuckerman 3815 4q12 GIST, AML, Familial L, M, Mis, O 4 feline sarcoma viral TGCT, gastrointestinal O, E oncogene homolog mastocytosis, stromal mucosal tumour melanoma KLK2 kallikrein-related 3817 19q13.41 prostate E T peptidase 2 KRAS v-Ki-ras2 Kirsten rat 3845 12p12.1 pancreatic, L, E, Mis sarcoma 2 viral colorectal, lung, M, O oncogene homolog thyroid, AML, others KTN1 kinectin 1 (kinesin 3895 14q22.1 papillary thryoid E T receptor) LAF4 lymphoid nuclear 3899 2q11.2-q12 ALL, T-ALL L T protein related to AF4 LASP1 LIM and SH3 protein 1 3927 17q11-q21.3 AML L T LCK lymphocyte-specific 3932 1p35-p34.3 T-ALL L T protein tyrosine kinase LCP1 lymphocyte cytosolic 3936 13q14.1-q14.3 NHL L T protein 1 (L-plastin) LCX leukemia-associated 80312 10q21 AML L T protein with a CXXC domain LHFP lipoma HMGIC fusion 10186 13q12 lipoma M T partner LIFR leukemia inhibitory 3977 5p13-p12 salivary E T factor receptor adenoma LMO1 LIM domain only 1 4004 11p15 T-ALL, L T, A (rhombotin 1) (RBTN1) neuroblastoma LMO2 LIM domain only 2 4005 11p13 T-ALL L T (rhombotin-like 1) (RBTN2) LPP LIM domain containing 4026 3q28 lipoma, L, M T preferred translocation leukemia partner in lipoma LRIG3 leucine-rich repeats 121227 12q14.1 NSCLC E T and immunoglobulin- like domains 3 LYL1 lymphoblastic 4066 19p13.2-p13.1 T-ALL L T leukemia derived sequence 1 MADH4 Homolog of Drosophila 4089 18q21.1 colorectal, Juvenile E D, Mis, N, F Mothers Against pancreatic, polyposis Decapentaplegic 4 small intestine gene MAF v-maf 4094 16q22-q23 MM L T musculoaponeurotic fibrosarcoma oncogene homolog MAFB v-maf 9935 20q11.2-q13.1 MM L T musculoaponeurotic fibrosarcoma oncogene homolog B (avian) MALT1 mucosa associated 10892 18q21 MALT L T lymphoid tissue lymphoma translocation gene 1 MAML2 mastermind-like 2 84441 11q22-q23 salivary gland E T (Drosophila) mucoepidermoid MAP2K4 mitogen-activated 6416 17p11.2 pancreatic, E D, Mis, N protein kinase kinase 4 breast, colorectal MDM2 Mdm2 p53 binding 4193 12q15 sarcoma, M, O, A protein homolog glioma, E, L colorectal, other MDM4 Mdm4 p53 binding 4194 1q32 GBM, bladder, M A protein homolog retinoblastoma MDS1 myelodysplasia 4197 3q26 MDS, AML L T syndrome 1 MDS2 myelodysplastic 259283 1p36 MDS L T syndrome 2 MECT1 mucoepidermoid 94159 19p13 salivary gland E T translocated 1 mucoepidermoid MED12 mediator complex 9968 Xq13 uterine M M, S subunit 12 leiomyoma MEN1 multiple endocrine 4221 11q13 parathyroid Multiple E D, Mis, N, neoplasia type 1 gene tumors, Endocrine F, S Pancreatic Neoplasia neuroendocrine Type 1 tumors MET met proto-oncogene 4233 7q31 papillary renal, Familial E Mis (hepatocyte growth head-neck Papillary factor receptor) squamous cell Renal Cancer MITF microphthalmia- 4286 3p14.1 melanoma E A associated transcription factor MKL1 megakaryoblastic 57591 22q13 acute L T leukemia megakaryocytic (translocation) 1 leukemia MLF1 myeloid leukemia 4291 3q25.1 AML L T factor 1 MLH1 E. coli MutL homolog 4292 3p21.3 colorectal, Hereditary E, O D, Mis, N, gene endometrial, non- F, S ovarian, CNS polyposis colorectal cancer, Turcot syndrome MLL myeloid/lymphoid or 4297 11q23 AML, ALL L T, O mixed-lineage leukemia (trithorax homolog, Drosophila) MLL2 myeloid/lymphoid or 8085 12q12-q14 medulloblastoma, O, E N, F, Mis mixed-lineage renal leukemia 2 MLL3 myeloid/lymphoid or 58508 7q36.1 medulloblastoma O N mixed-lineage leukemia 3 MLLT1 myeloid/lymphoid or 4298 19p13.3 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL) MLLT10 myeloid/lymphoid or 8028 10p12 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10) MLLT2 myeloid/lymphoid or 4299 4q21 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2 (AF4) MLLT3 myeloid/lymphoid or 4300 9p22 ALL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9) MLLT4 myeloid/lymphoid or 4301 6q27 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6) MLLT6 myeloid/lymphoid or 4302 17q21 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17) MLLT7 myeloid/lymphoid or 4303 Xq13.1 AL L T mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7 (AFX1) MN1 meningioma (disrupted 4330 22q13 AML, L, O T in balanced meningioma translocation) 1 MPL myeloproliferative 4352 p34 MPD Familial L Mis leukemia virus essential oncogene, thrombocythemia thrombopoietin receptor MSF MLL septin-like fusion 10801 17q25 AML* L T MSH2 mutS homolog 2 (E. coli) 4436 2p22-p21 colorectal, Hereditary E D, Mis, N, endometrial, non- F, S ovarian polyposis colorectal cancer MSH6 mutS homolog 6 (E. coli) 2956 2p16 colorectal Hereditary E Mis, N, F, S non- polyposis colorectal cancer MSI2 musashi homolog 2 124540 17q23.2 CML L T (Drosophila) MSN moesin 4478 Xq11.2-q12 ALCL L T MTCP1 mature T-cell 4515 Xq28 T cell L T proliferation 1 prolymphocytic leukemia MUC1 mucin 1, 4582 1q21 B-NHL L T transmembrane MUTYH mutY homolog (E. coli) 4595 1p34.3-1p32.1 Adenomatous E Mis polyposis coli MYB v-myb myeloblastosis 4602 6q22-23 adenoid cystic E T viral oncogene carcinoma homolog MYC v-myc 4609 8q24.12-q24.13 Burkitt L, E A, T myelocytomatosis viral lymphoma, oncogene homolog amplified in (avian) other cancers, B-CLL MYCL1 v-myc 4610 1p34.3 small cell lung E A myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) MYCN v-myc 4613 2p24.1 neuroblastoma O A myelocytomatosis viral related oncogene, neuroblastoma derived (avian) MYD88 myeloid differentiation 4615 3p22 ABC-DLBCL L Mis primary response gene (88) MYH11 myosin, heavy 4629 16p13.13-p13.12 AML L T polypeptide 11, smooth muscle MYH9 myosin, heavy 4627 22q13.1 ALCL L T polypeptide 9, non- muscle MYST4 MYST histone 23522 10q22 AML L T acetyltransferase (monocytic leukemia) 4 (MORF) NACA nascent-polypeptide- 4666 12q23-q24.1 NHL L T associated complex alpha polypeptide NBS1 Nijmegen breakage 4683 8q21 Nijmegen L, E, Mis, N, F syndrome 1 (nibrin) breakage M, O syndrome NCOA1 nuclear receptor 8648 2p23 alveolar M T coactivator 1 rhadomyosarcoma NCOA2 nuclear receptor 10499 8q13.1 AML, L T coactivator 2 (TIF2) Chondrosarcoma NCOA4 nuclear receptor 8031 10q11.2 papillary thyroid E T coactivator 4-PTC3 (ELE1) NDRG1 N-myc downstream 10397 8q24.3 prostate E T regulated 1 NF1 neurofibromatosis type 4763 17q12 neurofibroma, Neurofibroma O D, Mis, N, 1 gene glioma tosis type 1 F, S, O NF2 neurofibromatosis type 4771 22q12.2 meningioma, Neurofibroma O D, Mis, N, 2 gene acoustic tosis type 2 F, S, O neuroma, renal NFE2L2 nuclear factor 4780 2q31 NSCLC, E Mis (erythroid-derived 2)- HNSCC like 2 (NRF2) NFIB nuclear factor I/B 4781 9p24.1 adenoid cystic E T carcinoma, lipoma NFKB2 nuclear factor of kappa 4791 10q24 B-NHL L T light polypeptide gene enhancer in B-cells 2 (p49/p100) NIN ninein (GSK3B 51199 14q24 MPD L T interacting protein) NKX2-1 NK2 homeobox 1 7080 14q13 NSCLC E A NONO non-POU domain 4841 Xq13.1 papillary renal E T containing, octamer- cancer binding NOTCH1 Notch homolog 1, 4851 9q34.3 T-ALL L T, Mis, O translocation- associated (Drosophila) (TAN1) NOTCH2 Notch homolog 2 4853 1p13-p11 marginal zone L N, F, Mis lymphoma, DLBCL NPM1 nucleophosmin 4869 5q35 NHL, APL, AML L T, F (nucleolar phosphoprotein B23, numatrin) NR4A3 nuclear receptor 8013 9q22 extraskeletal M T subfamily 4, group A, myxoid member 3 (NOR1) chondrosarcoma NRAS neuroblastoma RAS 4893 1p13.2 melanoma, MM, L, E Mis viral (v-ras) oncogene AML, thyroid homolog NSD1 nuclear receptor 64324 5q35 AML L T binding SET domain protein 1 NTRK1 neurotrophic tyrosine 4914 1q21-q22 papillary thyroid E T kinase, receptor, type 1 NTRK3 neurotrophic tyrosine 4916 15q25 congenital E, M T kinase, receptor, type 3 fibrosarcoma, Secretory breast NUMA1 nuclear mitotic 4926 11q13 APL L T apparatus protein 1 NUP214 nucleoporin 214 kDa 8021 9q34.1 AML, T-ALL L T (CAN) NUP98 nucleoporin 98 kDa 4928 11p15 AML L T OLIG2 oligodendrocyte 10215 21q22.11 T-ALL L T lineage transcription factor 2 (BHLHB1) OMD osteomodulin 4958 9q22.31 aneurysmal M T bone cysts P2RY8 purinergic receptor 286530 Xp22.3; B-ALL, Downs L T P2Y, G-protein Yp11.3 associated ALL coupled, 8 PAFAH1B2 platelet-activating 5049 11q23 MLCLS L T factor acetylhydrolase, isoform lb, beta subunit 30 kDa PALB2 partner and localizer of 79728 16p12.1 Fanconianaemia L, O, E F, N, Mis BRCA2 N, breast cancer susceptibility PAX3 paired box gene 3 5077 2q35 alveolar M T rhabdomyosarcoma PAX5 paired box gene 5 (B- 5079 9p13 NHL, ALL, B- L T, Mis, D, cell lineage specific ALL F, S activator protein) PAX7 paired box gene 7 5081 p36.12 alveolar M T rhabdomyosarcoma PAX8 paired box gene 8 7849 2q12-q14 follicular thyroid E T PBRM1 polybromo 1 55193 3p21 clear cell renal E Mis, N, F, carcinoma, S, D, O breast PBX1 pre-B-cell leukemia 5087 1q23 pre B-ALL, L, M T transcription factor 1 myoepithelioma PCM1 pericentriolar material 5108 8p22-p21.3 papillary thyroid, E, L T 1 (PTC4) CML, MPD PCSK7 proprotein convertase 9159 11q23.3 MLCLS L T subtilisin/kexin type 7 PDE4DIP phosphodiesterase 4D 9659 1q12 MPD L T interacting protein (myomegalin) PDGFB platelet-derived growth 5155 22q12.3-q13.1 DFSP M T factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) PDGFRA platelet-derived growth 5156 4q11-q13 GIST, idiopathic L, M, O Mis, O, T factor, alpha-receptor hypereosinophilic syndrome, paediatric GBM PDGFRB platelet-derived growth 5159 5q31-q32 MPD, AML, L T factor receptor, beta CMML, CML polypeptide PER1 period homolog 1 5187 17p13.1-17p12 AML, CMML L T (Drosophila) PHF6 PHD finger protein 6 84295 Xq26.3 ETP ALL L F, N, Splice, Mis PHOX2B paired-like homeobox 8929 4p12 neuroblastoma familial O Mis, F 2b neuroblastoma PICALM phosphatidylinositol 8301 11q14 TALL, AML, L T binding clathrin assembly protein (CALM) PIK3CA phosphoinositide-3- 5290 3q26.3 colorectal, E, O Mis kinase, catalytic, alpha gastric, polypeptide gliobastoma, breast PIK3R1 phosphoinositide-3- 5295 5q13.1 gliobastoma, E, O Mis, F, O kinase, regulatory ovarian, subunit 1 (alpha) colorectal PIM1 pim-1 oncogene 5292 6p21.2 NHL L T PLAG1 pleiomorphic adenoma 5324 8q12 salivary E T gene 1 adenoma PML promyelocytic 5371 15q22 APL, ALL L T leukemia PMS1 PMS1 postmeiotic 5378 2q31-q33 Hereditary E Mis, N segregation increased non- 1 (S. cerevisiae) polyposis colorectal cancer PMS2 PMS2 postmeiotic 5395 7p22 Hereditary E Mis, N, F segregation increased non- 2 (S. cerevisiae) polyposis colorectal cancer, Turcot syndrome PMX1 paired mesoderm 5396 1q24 AML L T homeo box 1 PNUTL1 peanut-like 1 5413 22q11.2 AML L T (Drosophila) POU2AF1 POU domain, class 2, 5450 11q23.1 NHL L T associating factor 1 (OBF1) POU5F1 POU domain, class 5, 5460 6p21.31 sarcoma M T transcription factor 1 PPARG peroxisome 5468 3p25 follicular thyroid E T proliferative activated receptor, gamma PPP2R1A protein phosphatase 2, 5518 19q13.41 clear cell E Mis regulatory subunit A, ovarian alpha carcinoma PRCC papillary renal cell 5546 1q21.1 papillary renal E T carcinoma (translocation- associated) PRDM1 PR domain containing 639 6q21 DLBCL L D, N, Mis, 1, with ZNF domain F, S PRDM16 PR domain containing 63976 1p36.23-p33 MDS, AML L T 16 PRF1 perforin 1 (pore 5551 10q22 L M forming protein) PRKAR1A protein kinase, cAMP- 5573 17q23-q24 papillary thyroid Carney E, M T, Mis, N, dependent, regulatory, complex F, S type I, alpha (tissue specific extinguisher 1) PRO1073 PRO1073 protein 29005 11q31.1 renal cell E T (ALPHA) carcinoma (childhood epithelioid) PSIP2 PC4 and SFRS1 11168 9p22.2 AML L T interacting protein 2 (LEDGF) PTCH Homolog of Drosophila 5727 9q22.3 skin basal cell, Nevoid Basal E, M Mis, N, F, S Patched gene medulloblastoma Cell Carcinoma Syndrome PTEN phosphatase and 5728 10q23.3 glioma, Cowden L, E, D, Mis, N, tensin homolog gene prostate, Syndrome, M, O F, S endometrial Bannayan- Riley- Ruvalcaba syndrome PTPN11 protein tyrosine 5781 12q24.1 JMML, AML, L Mis phosphatase, non- MDS receptor type 11 RAB5EP rabaptin, RAB GTPase 9135 17p13 CMML L T binding effector protein 1 (RABPT5) RAD51L1 RAD51-like 1 (S. cerevisiae) 5890 14q23-q24.2 lipoma, uterine M T (RAD51B) leiomyoma RAF1 v-raf-1 murine 5894 3p25 pilocytic M T leukemia viral astrocytoma oncogene homolog 1 RALGDS ral guanine nucleotide 5900 9q34.3 PMBL, Hodgkin L T dissociation stimulator Lymphona, RANBP17 RAN binding protein 64901 5q34 ALL L T 17 RAP1GDS1 RAP1, GTP-GDP 5910 4q21-q25 T-ALL L T dissociation stimulator 1 RARA retinoic acid receptor, 5914 17q12 APL L T alpha RB1 retinoblastoma gene 5925 13q14 retinoblastoma, Familial L, E, D, Mis, N, sarcoma, retinoblastoma M, O F, S breast, small cell lung RBM15 RNA binding motif 64783 1p13 acute L T protein 15 megakaryocytic leukemia RECQL4 RecQ protein-like 4 9401 8q24.3 Rothmund- M N, F, S Thompson Syndrome REL v-rel 5966 2p13-p12 Hodgkin L A reticuloendotheliosis Lymphoma viral oncogene homolog (avian) RET ret proto-oncogene 5979 10q11.2 medullary Multiple E, O T, Mis, N, F thyroid, endocrine papillary thyroid, neoplasia pheochromocytoma, 2A/2B NSCLC ROS1 v-ros UR2 sarcoma 6098 6q22 glioblastoma, O, E T virus oncogene NSCLC homolog 1 (avian) RPL22 ribosomal protein L22 6146 1p36.31 AML, CML L T (EAP) RPN1 ribophorin I 6184 3q21.3-q25.2 AML L T RUNDC2A RUN domain 84127 16p13.13 PMBL, Hodgkin L T containing 2A Lymphona, RUNX1 runt-related 861 21q22.3 AML, preB- L T transcription factor 1 ALL, T-ALL (AML1) RUNXBP2 runt-related 7994 8p11 AML L T transcription factor binding protein 2 (MOZ/ZNF220) SBDS Shwachman-Bodian- 51119 7q11 Schwachman- L Gene Diamond syndrome Diamond Conversion protein syndrome SDC4 syndecan 4 6385 20q12 NSCLC E T SDH5 chromosome 11 open 54949 11q12.2 Familial M M reading frame 79 paraganglioma SDHB succinate 6390 1p36.1-p35 Familial O Mis, N, F dehydrogenase paraganglioma complex, subunit B, iron sulfur (Ip) SDHC succinate 6391 1q21 Familial O Mis, N, F dehydrogenase paraganglioma complex, subunit C, integral membrane protein, 15 kDa SDHD succinate 6392 11q23 Familial O Mis, N, F, S dehydrogenase paraganglioma complex, subunit D, integral membrane protein SEPT6 septin 6 23157 Xq24 AML L T SET SET translocation 6418 9q34 AML L T SETD2 SET domain 29072 3p21.31 clear cell renal E N, F, S, containing 2 carcinoma Mis SF3B1 splicing factor 3b, 23451 2q33.1 myelodysplastic L Mis subunit 1, 155 kDa syndrome SFPQ splicing factor 6421 1p34.3 papillary renal E T proline/glutamine cell rich(polypyrimidine tract binding protein associated) SFRS3 splicing factor, 6428 6p21 follicular L T arginine/serine-rich 3 lymphoma SH3GL1 SH3-domain GRB2- 6455 19p13.3 AL L T like 1 (EEN) SIL TAL1 (SCL) 6491 1p32 T-ALL L T interrupting locus SLC34A2 solute carrier family 34 10568 4p15.2 NSCLC E T (sodium phosphate), member 2 SLC45A3 solute carrier family 85414 1q32 prostate E T 45, member 3 SMARCA4 SWI/SNF related, 6597 19p13.2 NSCLC E F, N, Mis matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 SMARCB1 SWI/SNF related, 6598 22q11 malignant Rhabdoid M D, N, F, S matrix associated, rhabdoid predisposition actin dependent syndrome regulator of chromatin, subfamily b, member 1 SMO smoothened homolog 6608 7q31-q32 skin basal cell E Mis (Drosophila) SOCS1 suppressor of cytokine 8651 16p13.13 Hodgkin L F, O signaling 1 Lymphoma, PMBL SOX2 SRY (sex determining 6657 3q26.3-q27 NSCLC, E A region Y)-box 2 oesophageal squamous carcinoma SRGAP3 SLIT-ROBO Rho 9901 3p25.3 pilocytic M T GTPase activating astrocytoma protein 3 SRSF2 serine/arginine-rich 6427 17q25 MDS, CLL L Mis splicing factor 2 SS18 synovial sarcoma 6760 18q11.2 synovial M T translocation, sarcoma chromosome 18 SS18L1 synovial sarcoma 26039 20q13.3 synovial M T translocation gene on sarcoma chromosome 18-like 1 SSH3BP1 spectrin SH3 domain 10006 10p11.2 AML L T binding protein 1 SSX1 synovial sarcoma, X 6756 Xp11.23-p11.22 synovial M T breakpoint 1 sarcoma SSX2 synovial sarcoma, X 6757 Xp11.23-p11.22 synovial M T breakpoint 2 sarcoma SSX4 synovial sarcoma, X 6759 Xp11.23 synovial M T breakpoint 4 sarcoma STK11 serine/threonine 6794 19p13.3 NSCLC, Peutz- E, M, O D, Mis, N, kinase 11 gene (LKB1) pancreatic Jeghers F, S syndrome STL Six-twelve leukemia 7955 6q23 B-ALL L T gene SUFU suppressor of fused 51684 10q24.32 medulloblastoma Medulloblastoma O D, F, S homolog (Drosophila) predisposition SUZ12 suppressor of zeste 12 23512 17q11.2 endometrial M T homolog (Drosophila) stromal tumours SYK spleen tyrosine kinase 6850 9q22 MDS, peripheral L T T-cell lymphoma TAF15 TAF15 RNA 8148 17q11.1-q11.2 extraskeletal L, M T polymerase II, TATA myxoid box binding protein chondrosarcomas, (TBP)-associated ALL factor, 68 kDa TAL1 T-cell acute 6886 1p32 lymphoblastic L T lymphocytic leukemia leukemia/biphasic 1 (SCL) TAL2 T-cell acute 6887 9q31 T-ALL L T lymphocytic leukemia 2 TCEA1 transcription 6917 8q11.2 salivary E T elongation factor A adenoma (SII), 1 TCF1 transcription factor 1, 6927 12q24.2 hepatic Familial E Mis, F hepatic (HNF1) adenoma, Hepatic hepatocellular Adenoma ca TCF12 transcription factor 12 6938 15q21 extraskeletal M T (HTF4, helix-loop-helix myxoid transcription factors 4) chondrosarcoma TCF3 transcription factor 3 6929 19p13.3 pre B-ALL L T (E2A immunoglobulin enhancer binding factors E12/E47) TCF7L2 transcription factor 7- 6934 10q25.3 colorectal E T like 2 TCL1A T-cell 8115 14q32.1 T-CLL L T leukemia/lymphoma 1A TCL6 T-cell 27004 14q32.1 T-ALL L T leukemia/lymphoma 6 TET2 tet oncogene family 54790 4q24 MDS L Mis N, F member 2 TFE3 transcription factor 7030 Xp11.22 papillary renal, E T binding to IGHM alveolar soft enhancer 3 part sarcoma, renal TFEB transcription factor EB 7942 6p21 renal (childhood E, M T epithelioid) TFG TRK-fused gene 10342 3q11-q12 papillary thyroid, E, L T ALCL, NSCLC TFPT TCF3 (E2A) fusion 29844 19q13 pre-B ALL L T partner (in childhood Leukemia) TFRC transferrin receptor 7037 3q29 NHL L T (p90, CD71) THRAP3 thyroid hormone 9967 1p34.3 aneurysmal M T receptor associated bone cysts protein 3 (TRAP150) TIF1 transcriptional 8805 7q32-q34 APL L T intermediary factor 1 (PTC6, TIF1A) TLX1 T-cell leukemia, 3195 10q24 T-ALL L T homeobox 1 (HOX11) TLX3 T-cell leukemia, 30012 5q35.1 T-ALL L T homeobox 3 (HOX11L2) TMPRSS2 transmembrane 7113 21q22.3 prostate E T protease, serine 2 TNFAIP3 tumor necrosis factor, 7128 6q23 marginal zone L D, N, F alpha-induced protein 3 B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma TNFRSF14 tumor necrosis factor 8764 1p36.32 follicular L Mis, N, F receptor superfamily, lymphoma member 14 (herpesvirus entry mediator) TNFRSF17 tumor necrosis factor 608 16p13.1 intestinal T-cell L T receptor superfamily, lymphoma member 17 TNFRSF6 tumor necrosis factor 355 10q24.1 TGCT, nasal L, E, O Mis receptor superfamily, NK/T member 6 (FAS) lymphoma, skin squamous cell ca-burn scar- related TOP1 topoisomerase (DNA) I 7150 20q12-q13.1 AML* L T breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple TP53 tumor protein p53 7157 17p13 other tumour Li-Fraumeni L, E, Mis, N, F types syndrome M, O TPM3 tropomyosin 3 7170 1q22-q23 papillary thyroid, E, L T ALCL, NSCLC TPM4 tropomyosin 4 7171 19p13.1 ALCL L T TPR translocated promoter 7175 1q25 papillary thyroid E T region TRA@ T cell receptor alpha 6955 14q11.2 T-ALL L T locus TRB@ T cell receptor beta 6957 7q35 T-ALL L T locus TRD@ cell receptor delta 6964 14q11 T-cell leukemia L T locus TRIM27 tripartite motif- 5987 6p22 papillary thyroid E T containing 27 TRIM33 tripartite motif- 51592 1p13 papillary thyroid E T containing 33 (PTC7, TIF1G) TRIP11 thyroid hormone 9321 14q31-q32 AML L T receptor interactor 11 TSC1 tuberous sclerosis 1 7248 9q34 Tuberous E, O D, Mis, N, gene sclerosis 1 F, S TSC2 tuberous sclerosis 2 7249 16p13.3 Tuberous E, O D, Mis, N, gene sclerosis 2 F, S TSHR thyroid stimulating 7253 14q31 toxic thyroid E Mis hormone receptor adenoma TTL tubulin tyrosine ligase 150465 2q13 ALL L T U2AF1 U2 small nuclear RNA 7307 21q22.3 CLL, MDS L Mis auxiliary factor 1 USP6 ubiquitin specific 9098 17p13 aneurysmal M T peptidase 6 (Tre-2 bone cysts oncogene) VHL von Hippel-Lindau 7248 3p25 renal, von Hippel- E, M, O D, Mis, N, syndrome gene hemangioma, Lindau F, S pheochromocytoma syndrome VTI1A vesicle transport 143187 10q25.2 colorectal E T through interaction with t-SNAREs homolog 1A WAS Wiskott-Aldrich 7454 Xp11.23-p11.22 Wiskott- L Mis, N, F, S syndrome Aldrich syndrome WHSC1 Wolf-Hirschhorn 7468 4p16.3 MM L T syndrome candidate 1(MMSET) WHSC1L1 Wolf-Hirschhorn 54904 8p12 AML L T syndrome candidate 1- like 1 (NSD3) WIF1 WNT inhibitory factor 1 11197 12q14.3 pleomorphic E T salivary gland adenoma WRN Werner syndrome 7486 8p12-p11.2 Werner L, E, Mis, N, F, S (RECQL2) Syndrome M, O WT1 Wilms tumour 1 gene 7490 11p13 Wilms, Denys-Drash O D, Mis, N desmoplastic syndrome, F, S small round cell Frasier tumor syndrome, Familial Wilms tumour WTX family with sequence 139285 Xq11.1 Wilms tumour O F, D, N, similarity 123B Mis (FAM123B) WWTR1 WW domain containing 607392 3q23-q24 epitheliod M T transcription regulator 1 hemangioendot helioma XPA xeroderma 7507 9q22.3 Xeroderma E Mis, N, F, S pigmentosum, pigmentosum complementation (A) group A XPC xeroderma 7508 3p25 Xeroderma E Mis, N, F, S pigmentosum, pigmentosum complementation (C) group C XPO1 exportin 1 (CRM1 7514 2p15 CLL L Mis homolog, yeast) YWHAE tyrosine 3- 7531 17p13.3 edometrial M T monooxygenase/tryptophan stromal 5- sarcoma monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon) ZNF145 zinc finger protein 145 7704 11q23.1 APL L T (PLZF) ZNF198 zinc finger protein 198 7750 13q11-q12 MPD, NHL L T ZNF278 zinc finger protein 278 23598 22q12-q14 Ewing sarcoma M T (ZSG) ZNF331 zinc finger protein 331 55422 19q13.3-q13.4 follicular thyroid E T adenoma ZNF384 zinc finger protein 384 171017 12p13 ALL L T (CIZ/NMP4) ZNF521 zinc finger protein 521 25925 18q11.2 ALL L T ZNF9 zinc finger protein 9 (a 7555 3q21 aneurysmal M T cellular retroviral bone cysts nucleic acid binding protein) ZRSR2 zinc finger (CCCH 8233 Xp22.1 MDS, CLL L F, S, Mis type), RNA-binding motif and serine/arginine rich 2

The following abbreviations are used in the table above: A, amplification; AEL, acute eosinophilic leukemia; AL, acute leukemia; ALCL, anaplastic large-cell lymphoma; ALL, acute lymphocytic leukemia; AML, acute myelogenous leukemia; AML*, acute myelogenous leukemia (primarily treatment associated); APL, acute promyelocytic leukemia; B-ALL, B-cell acute lymphocytic leukaemia; B-CLL, B-cell Lymphocytic leukemia; B-NHL, B-cell Non-Hodgkin Lymphoma; CLL, chronic lymphatic leukemia; CML, chronic myeloid leukemia; CMML, chronic myelomonocytic leukemia; CNS, central nervous system; D, large deletion; DFSP, dermatofibrosarcoma protuberans; DLBCL, diffuse large B-cell lymphoma; DLCL, diffuse large-cell lymphoma; Dom, dominant; E, epithelial; F frameshift; GIST, gastrointestinal stromal tumour; JMML, juvenile myelomonocytic leukemia; L, leukemia/lymphoma; M, mesenchymal; MALT, mucosa-associated lymphoid tissue lymphoma; MDS, myelodysplastic syndrome; Mis, Missense; MLCLS mediastinal large cell lymphoma with sclerosis; MM, multiple myeloma; MPD, Myeloproliferative disorder; N, nonsense; NHL, non-Hodgkin lymphoma; NK/T, natural killer T cell; NSCLC, non small cell lung cancer; O, other; PMBL, primary mediastinal B-cell lymphoma; pre-B All, pre-B-cell acute lymphoblastic leukaemia; Rec, recessive; S, splice site; T, translocation; T-ALL, T-cell acute lymphoblastic leukemia; T-CLL, T-cell chronic lymphocytic leukaemia; TGCT, testicular germ cell tumour; T-PLL, T cell prolymphocytic leukaemia. It is contemplated that a padlock probe can be designed in order to detect a mutation in a cancer gene listed in the table above. A padlock probe can have a sequence that is complementary to a mutation, which may be a substitution of one or more nucleotides for one or more wild-type nucleotides in a mRNA sequence, a deletion of one or more nucleotides compared to a wild-type mRNA sequence, an addition of one or more nucleotides compared to a wild-type mRNA sequence, a sequence inversion, a sequence translocation, a frameshift, or other mutation. With many cancer mutations, the mutation has been previously characterized, including with inversions and translocations such that sequence design is possible.

H. Kits

Also provided are kits for use in methods described herein. The kit may comprise at least one (species of) padlock probe, as defined above, specific for a particular cDNA. Such a kit may also comprise RT primer(s), an RT enzyme, a ribonuclease, a DNA polymerase, a ligase and/or means of detection of RCA product.

The kit may optionally further comprise one or more gap oligonucleotides with complementarity to the portion of the target cDNA which lies between non-adjacently-hybridized padlock probe ends or may comprise reagents for otherwise filling any gap present when the ends of the padlock probe are hybridized to the cDNA, such as a polymerase, nucleotides and necessary co-factors. In some embodiments, the kit may further comprises a primer oligonucleotide for priming RCA of the padlock probe. In certain aspects, the primer hybridizes to the padlock probe at a location other than the region(s) of the padlock probe that is complementary to the target cDNA.

Alternatively or additionally, the kit may comprise a ligase for circularizing the padlock probe(s) (which may or may not be present in the kit) or a polymerase such as phi29 polymerase (and optionally necessary cofactors, as well and nucleotides) for effecting RCA. Reagents for detecting the RCA product may also be included in the kit. Such reagents may include a labeled oligonucleotide hybridization probe having complementarity to a portion of a padlock probe, or to a portion of a gap oligonucleotide, present in the kit.

The kit may be designed for use in multiplex embodiments of the different method embodiments, and accordingly may comprise combinations of the components defined above for more than target RNA. If probes having binding specificity respectively for a plurality of cDNA species are present in the kit, the kit may additionally comprise components allowing multiple RNA detection in parallel to be distinguished. For example, the kit may contain padlock probes for different cDNA targets, wherein the cDNA targets have “unique” sequences for hybridization only to a particular species of probe. Such padlock probes may for example carry different tag or identifier sequences allowing the detection of different RNAs to be distinguished.

The kit may be designed for use in the detection of an mRNA coding for KRAS. In some embodiments, the kit may contain one or more padlock probes that target cDNA reverse transcribed from the wild-type KRAS mRNA and/or one or more padlock probes which target cDNA reverse transcribed from a KRAS mRNA molecule comprising a point-mutation.

In addition to the above components, the kit may further include instructions for practicing method embodiments. These instructions may be present in the kit in a variety of forms, one or more of which may be present in the kit. One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc. Yet another means would be a computer readable medium, e.g., diskette, CD, etc., on which the information has been recorded. Yet another means that may be present is a website address which may be used via the internet to access the information at a remote site. Any convenient means may be present in the kit.

Thus, in a further aspect a kit is provided for use in the localized in situ detection of a target RNA in a sample, the kit comprising one or more components selected from the list comprising:

(i) a padlock probe comprising 3′ and 5′ terminal regions having complementarity to cDNA transcribed from the target RNA (such regions can alternatively be defined as corresponding in sequence to regions of the target RNA, which regions as defined above may be adjacent or non-adjacent);

(ii) a reverse transcriptase primer capable of hybridizing to the target RNA (e.g. capable of hybridizing specifically to the RNA);

(iii) a reverse transcriptase;

(iv) a ribonuclease;

(v) a ligase;

(vi) a polymerase having 3′ exonuclease activity;

(vii) a gap oligonucleotide capable of hybridizing to a portion of a cDNA transcribed from the target RNA;

(viii) a detection probe capable of hybridizing to a complement of a padlock probe of (i); or to a complement of a gap oligonucleotide of (vii);

(ix) nucleotides for incorporation e.g. dNTPs.

The detection probe of (viii) may be a labeled detection oligonucleotide capable of hybridizing to the amplification product (which will contain a complement of a padlock probe of (i) or a complement of a gap oligonucleotide of (vii)). For example the detection oligonucleotide may be fluorescently labeled or may be labeled with a horse radish-peroxidase.

In one embodiment the kit may contain the padlock probe of (i) and optionally one or more further components selected from any one of (ii) to (ix). Other combinations of kit components are also possible. For example the kit may contain the padlock probe of (i) and at least one of the reverse transcriptase primer of (ii), the reverse transcriptase of (iii) and the ribonuclease of (iv), optionally with one or more further components selected from any one of (ii) or (iii) or (iv) to (ix). Other representative kits may include the reverse transcriptase primer of (ii), and at least one of components (iii) to (ix), more particularly the primer of (ii) with at least one of components ((iii) to (vi), and optionally with one or more further components selected from any one of (i) or (vii) to (ix). Also included by way of representative example is a kit comprising at least two, or at least three, or all four, of components (iii) to (vi), optionally together with one or more further components selected from (i), (ii), or (vii) to (ix). All possible combinations of 2 or 3 components selected from (iii) to (iv) are covered. For example, such an embodiment may include (iii), (iv) and (v), or (iii), (v) and (vi), or (iii), (iv) and (vi) and so on.

In additional embodiments, kits may contain one or more reagents for sequencing after rolling circle amplification.

I. Tables

TABLE 1  Oligonucleotide sequences SEQ Name Sequence NOS: cDNA primers P-βe1^(a) A+TC+AT+CC+AT+GG+TG+AGCTGGCGGCGG 32 P-βhum^(a) C+TG+AC+CC+AT+GC+CC+ACCATCACGCCC 33 P-βmus C+TG+AC+CC+AT+TC+CC+ACCATCACACCC 34 P-βe6 T+TA+GA+GA+GA+AG+TG+GGGTGGCTTTTA 35 P-cMyc^(a) G+CG+TC+CT+TG+CT+CG+GGTGTTGTAAGTTCCAG 36 P-HER2^(a) G+AG+CT+GG+GT+GC+CT+CGCACAATCCGCAGCCT 37 P-TERT^(a) A+GG+AC+AC+CT+GG+CG+GAAGGAGGGGGCGGCGG 38 P-α1βmus^(a) A+CT+CG+TC+AT+AC+TC+CTGCTTGCTGATCCACA 39 P-γ1mus^(a) G+CC+TC+AG+GA+AA+TC+CTGGAAGTCTGC 40 Padlock probes PLP-βe1^(b )(DP-1) AGCCTCGCCTTTGCCTTCCTTTTACGACCTCAATGCTG 41 (detection probe) CTGCTGTACTA CTCTTCGCCCCGCGAGCACAG PLP-βhum^(a) (DP-4) GCCGGCTTCGCGGGCGACGATTCCTCTATGATTACTG 42 ACCTATGCGTCTATTTAGTGGAGCCTCTTCTTTACGGC GCCGGCATGTGCAAG PLP-βmus^(a) (DP-5) GCCGGCTTCGCGGGCGACGATTCCTCTATGATTACTG 43 ACCTAAGTCGGAAGTACTACTCTCTTCTTCTTTACGGC GCCGGCATGTGCAAA PLP-βe6^(a) (DP-1) TACAGGAAGTCCCTTGCCATTTCCTCTATGATTACTGA 44 CCTACCTCAATGCTGCTGCTGTACTACTCTTCCCAAAG ATGAGATGCGTTGT PLP2-βmus^(c) (DP-3) CTGTCCACCTTCCAGAGAGTGTACCGACCTCAGTAAG 45 TAGCCGTGACTATCGACTTCCAGCCTGGCCTCA PLP-α1mus^(c) (DP-2) CTGTCCACCTTCCAGCCTTTCCTACGACCTCAATGCAC 46 ATGTTTGGCTCCTCTTCTCCAGCCTGGCCTCG PLP-γ1mus^(a) (DP-1) CCCCAGCCTGGTGGAAGCTAGCTACCTCAATGCTGCT 47 GCTGTACTACTATGACTGCTGGAGATGAGAAAG PLP-cMyc^(c) (DP-4) CGAAACTTTGCCCATAGCAGATTGGAACGTTTAAATG 48 CGTCTATTTAGTGGAGCCGAGACAATCTTACATCGCA ACCCTTGCCGCATCCA PLP-HER2^(c) (DP-5) TGCCAGCCTGTCCTTCCTGCATCGTCTTAATCACTAGT 49 CGGAAGTACTACTCTCTTACGCTTACAACTAGCTCAC CTACCTGCCCACCAA PLP-TERT^(c) (DP-2) GGTGTGCGTGCCCTGGGACGACTTTCTATGATTACTG 50 ACCTACCTCAATGCACATGTTTGGCTCCTCTTCGCGCT GGTGGCCCAGTGCCT PLP-KRAS-wtGGT³ GGCGTAGGCAAGAGTTCCTGTAGTAAAGTAGCCGTGA 51 (DP-3) CTATCGACTGAATCTAAGGTAGTTGGAGCTGGT PLP-KRAS- GGCGTAGGCAAGAGTGTAAGTCATCAAGTCGGAAGT 52 mutGAT³ (DP-5) ACTACTCTCTGAATCTAAGGTAGTTGGAGCTGTT Detection probes DP-1Cy3^(d) Cy3-CCTCAATGCTGCTGCTGTACTAC 53 DP-1Cy3.5^(a) TexasRed-CCTCAATGCTGCTGCTGTACTAC 53 DP-2FITC^(a) FITC-CCTCAATGCACATGTTTGGCTCC 54 DP-2Cy5⁹ Cy5-CCTCAATGCACATGTTTGGCTCC 54 DP-3^(d) Cy3-AGTAGCCGTGACTATCGACT 55 DP-4^(c) Cy3-TGCGTCTATTTAGTGGAGCC 56 DP-5^(d) Cy5-AGTCGGAAGTACTACTCTCT 57 qPCR primers ACTBfwd^(b) CTGGAACGGTGAAGGTGACA 58 ACTBrev^(b) CGGCCACATTGTGAACTTTG 59 Oligonucleotides are given in 5′-3′ order + symbol denotes the LNA bases Oligonucleotides were purchased from Integrated DNA Technologies³, DNA technology A/S^(b), Biomers^(c) and Eurogentec^(d)

TABLE 2  Sequences of cDNA primers for LNA content investigation SEQ Primer LNA content Sequence NOS: P-unmod No LNA ATCATCCATGGTGAGCTGGCGGCGG 32 P-LNA1 or 7 LNA, every A+TC+AT+CC+AT+GG+TG+AGCTGGCGGCGG 32 P-βe1 2^(nd) P-LNA2 7 LNA, every A+TC+AT+CC+AT+GG+TG+AGCTGGCGGCGGGTGTG 60 2^(nd) P-LNA3 9 LNA, every A+TC+AT+CC+AT+GG+TG+AG+CT+GGCGGCGGGTGTG 60 2^(nd) P-LNA4 5 LNA, every A+TC+AT+CC+AT+GGTGAGCTGGCGGCGGGTGTG 60 2^(nd) P-LNA5 5 LNA, every AT+CAT+CCA+TGG+TGA+GCTGGCGGCGGGTGTG 60 3^(rd)

Oligonucleotides are given in 5′-3′ order. + symbol denotes the LNA bases.

All LNA containing Oligonucleotides were purchased from Integrated DNA Technology. The unmodified primer was purchased from Biomers.

TABLE 3  Sequences of cDNA primers for investigation of cDNA synthesis length SEQ Primer Sequence NOS: P-93 nt or P-βe1 A+TC+AT+CC+AT+GG+TG+AGCTGGCGGCGG 32 P-141 nt G+GC+CT+TG+CA+CA+TG+CCGGAGCCGTTGTCGAC 61 P-231 nt or P-βhum C+TG+AC+CC+AT+GC+CC+ACCATCACGCCC 33 P-261 nt C+TG+GG+CC+TC+GT+CG+CCCACATAGGAATCCTT 62 P-501 nt C+AC+AG+CC+TG+GA+TA+GCAACGTACATGGCTGG 63

Oligonucleotides are given in 5′-3′ order. + symbol denotes the LNA base

Oligonucleotides were purchased from Integrated DNA Technology.

The primer name indicates the maximum length of the produced cDNA for each respective cDNA primer.

TABLE 4  Oligonucleotide sequences for genotyping of KRAS mutations SEQ Oligonucleotide sequences ID Sequences (5′-3′) NOs Primers P-KRAS-c12/13^(b) T+GT+AT+CG+TC+AA+GG+CACTCTT 64 P-KRAS-c12/13- C+CT+CT+AT+TG+TT+GG+ATCATATTCGTC 65 II^(a) P-KRAS-Q61H^(b) T+AT+TC+GT+CC+AC+AA+AATGATTCTGAA 66 P-EGFR-L858R^(b) T+CT+TT+CT+CT+TC+CG+CACCCAG 67 P-EGFR-S768I^(b) G+GC+GG+CA+CA+CGTGGGGGTTG 68 P-EGFR- C+CT+TA+TA+CA+CC+GT+GCCGAAC 69 G719C/A^(b) P-TP53-S127F^(b) A+GT+TG+GC+AA+AA+CA+TCTTGTTGAGGG 70 P-TP53-P190S^(b) T+TC+CT+TC+CA+CT+CG+GATAAGATGCTG 71 P-ACTB^(b) G+TG+GA+CG+GG+CG+GC+GGATCGGCAAAG 72 P-ACTB-II^(b) A+TC+AT+CC+AT+GG+TG+AGCTGGCGGCGG 73 Padlock probes PP-KRAS-wt1^(a) GTGGCGTAGGCAAGATCCTAGTAATCAGTAGCCGTGACTATCGAC 74 (DP-1) TGGTTCAAAGTGGTAGTTGGAGCTG PP-KRAS-G12S^(a) GTGGCGTAGGCAAGATTCTAGATCCCTCAATGCACATGTTTGGCTC 75 (DP-2) CGGTTCAAGTGGTAGTTGGAGCTA PP-KRAS-G12R^(a) GTGGCGTAGGCAAGATTCTAGATCCCTCAATGCACATGTTTGGCTC 76 (DP-2) CGGTTCAAGTGGTAGTTGGAGCTC PP-KRAS-G12C^(a) GTGGCGTAGGCAAGATTCTAGATCCCTCAATGCACATGTTTGGCTC 77 (DP-2) CGGTTCAAGTGGTAGTTGGAGCTT PP-KRAS-wt2^(a) TGGCGTAGGCAAGAGTCCTAGTAATCAGTAGCCGTGACTATCGAC 78 (DP-1) TGGTTCAAAGGGTAGTTGGAGCTGG PP-KRAS-G12D^(a) TGGCGTAGGCAAGAGTTCTAGATCCCTCAATGCACATGTTTGGCTC 79 (DP-2) CGGTTCAAGGGTAGTTGGAGCTGA PP-KRAS-G12V^(a) TGGCGTAGGCAAGAGTTCTAGATCCCTCAATGCACATGTTTGGCTC 80 (DP-2) CGGTTCAAGGGTAGTTGGAGCTGT PP-KRAS-G12A^(a) TGGCGTAGGCAAGAGTTCTAGATCCCTCAATGCACATGTTTGGCTC 81 (DP-2) CGGTTCAAGGGTAGTTGGAGCTGC PP-KRAS-wt3^(a) CGTAGGCAAGAGTGCTCCTAGTAATCAGTAGCCGTGACTATCGAC 82 (DP-1) TGGTTCAAAGAGTTGGAGCTGGTGG PP-KRAS-G13D^(a) CGTAGGCAAGAGTGCTTCTAGATCCCTCAATGCACATGTTTGGCTC 83 (DP-2) CGGTTCAAGAGTTGGAGCTGGTGA PP-KRA S-wt4^(a) GAGGAGTACAGTGCATCCTAGTAATCAGTAGCCGTGACTATCGAC 84 (DP-1) TGGTTCAAAGGACACAGCAGGTCAA PP-KRAS-Q61H^(a) GAGGAGTACAGTGCACGCTAGATCCCTCAATGCACATGTTTGGCT 85 (DP-2) CCGGTTCAAGGACACAGCAGGTCAT PP-EGFR-wt1^(a) GGCCAAACTGCTGGGTCCTAGTAATCAGTAGCCGTGACTATCGAC 86 (DP-1) TGGTTCAAAGCACAGATTTTGGGCT PP-EGFR-L858R^(a) GGCCAAACTGCTGGGTTCTAGATACCTCAATGCTGCTGCTGTACTA 87 (DP-3) CGGTTCAAGCACAGATTTTGGGCG PP-EGFR-wt2^(a) CGTGGACAACCCCCATCCTAGTAATCAGTAGCCGTGACTATCGAC 88 (DP-1) TGGTTCAAAGCTACGTGATGGCCAG PP-EGFR-S768I^(a) CGTGGACAACCCCCATTCTAGATACCTCAATGCTGCTGCTGTACTA 89 (DP-3) CGGTTCAAGCTACGTGATGGCCAT PP-EGFR-wt3^(a) GCTCCGGTGCGTTCGTCCTAGTAATCAGTAGCCGTGACTATCGACT 90 (DP-1) GGTTCAAAGAGATCAAAGTGCTGG PP-EGFR-G719C^(a) GCTCCGGTGCGTTCGTTCTAGATCCCTCAATGCACATGTTTGGCTC 91 (DP-2) CGGTTCAAGAGATCAAAGTGCTGT PP-EGFR-wt4^(a) CTCCGGTGCGTTCGGTCCTAGTAATCAGTAGCCGTGACTATCGACT 92 (DP-1) GGTTCAAAGGATCAAAGTGCTGGC PP-EGFR-G719A^(a) CTCCGGTGCGTTCGGTTCTAGATCCCTCAATGCACATGTTTGGCTC 93 (DP-2) CGGTTCAATGATCAAAGTGCTGGG PP-TP53-wt1^(a) CCCTGCCCTCAACAATTCCTTTTACGACCTCAATGCTGCTGCTGTA 94 (DP-3) CTACTCTTCGACTTGCACGTACTC PP-TP53-S127F^(a) CCCTGCCCTCAACAACTAGTATCTGAGTCGGAAGTACTACTCTCTT  95 (DP-4) GTGCCATAAGACTTGCACGTACTT PP-TP53-wt2^(a) CTCCTCAGCATCTTATTCCTTTTACGACCTCAATGCTGCTGCTGTA 96 (DP-3) CTACTCTTCGCGATGGTCTGGCCC PP-TP53-P190S^(a) CTCCTCAGCATCTTACTAGTATCTGAGTCGGAAGTACTACTCTCTT 97 (DP-4) GTGCCATAAGCGATGGTCTGGCCT PP-ACTB^(a) AGCCTCGCCTTTGCCTTCCTTTTACGACCTCAATGCTGCTGCTGTA 98 (DP-3) CTACTCTTCGCCCCGCGAGCACAG PP-ACTB-II^(a) AGCCTCGCCTTTGCCTTCCTTTTACGACCTCAATGCACATGTTTGG 99 (DP-2) CTCCTCTTCGCCCCGCGAGCACAG Detection probes DP-1^(d) AGTAGCCGTGACTATCGACT 55 DP-2^(d) CCTCAATGCACATGTTTGGCTCC 54 DP-3^(c) CCTCAATGCTGCTGCTGTACTAC 53 DP-4^(a) AGTCGGAAGTACTACTCTCT 57 + = LNA-modified base, underline = target complementary sequence, italic = detection probe complementary sequence Oligonucleotides were purchased from Integrated DNA Technologies^(a), Exiqon^(b), Biomers^(c) and Eurogentec^(d).

TABLE 5 Summary of samples that were genotyped for KRAS mutations Mutation analysis of fresh frozen, FFPE and tumor imprint samples 2. In situ padlock probe Sample 1. Pyrosequencing mutation detection ID Sample Type Target Mutants/Total Mutations Mutants/Total Concordance 1-5 Fresh frozen colon KRAS 4/5 1xG12D, 1xG12C, 4/5 100% 1xG13D, 1xG12A  6-10 Fresh frozen lung KRAS 4/5 1xG12D, 1xG12V, 4/5 100% 1xG12C, 1xG12S 11-24 FFPE colon KRAS 14/14 2xG12D, 3xG12V, 14/14 100% 2xG12C, 3xG13D, 2xG12S, 1xG12A 25-26 FFPE lung KRAS 2/2 2xQ61H 2/2 100% 27-35 FFPE lung EGFR 8/9 8xL858R 8/9 100% 36 FFPE lung EGFR 1/1 1xG719C, 1xS768I 1/1 100% 37 FFPE lung EGFR/TP53 1/1 1xG719A, 1xS127F 1/1 100% 38 FFPE lung KRAS/TP53 1/1 1xG12C, 1xP190S 1/1 100% Mutation analysis of prospective FFPE and tumor imprint samples 1. In situ padlock probe mutation detection 2. Pyrosequencing Sample ID Sample Type Target Mutants/Total Mutants/Total Mutations Concordance 39-46 FFPE lung KRAS 3/8 3/8 2xG12C, 100% 1xG12R 47-54 Colon tumor imprint KRAS 2/8 2/8 1xG12D, 100% 1xG12R 55-79 FFPE colon (from TMA) KRAS 11/25 11/25 6xG12V, 100% 2xG12S, 2xG13D, 1xG12A

TABLE 6 Oligonucleotides on samples Primers Padlock probes Detection probes Sample ID  1 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12D  2 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt1 G12C  3 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt3 G13D  4 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12A  5 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12A  6 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12D  7 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12V  8 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt1 G12C  9 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt1 G12S 10 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12A 11-12 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12D 13-15 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12V 16-17 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt1 G12C 18-20 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt3 G13D 21-22 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt1 G12S 23-24 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt2 G12A 25-26 P-KRAS-Q61H P-ACTB PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 wt4 Q61H 27-35 P-EGFR-L858R P-ACTB PP-EGFR- PP-EGFR- PP-ACTB-II DP-1 DP-3 DP-2 wt1 L858R 36 P-EGFR-S768I P-EGFR- PP-EGFR- PP-EGFR- PP-EGFR- PP-EGFR- DP-1 DP-3 DP-2 G719C/A wt2 S768I wt3 G719C 37 P-EGFR- P-TP53-S127F PP-EGFR- PP-EGFR- PP-TP53-wt1 PP-TP53- DP-1 DP-2 DP-3 DP-4 G719C/A wt4 G719A S127F 38 P-KRAS-c12/13 P-TP53-P190S PP-KRAS- PP-KRAS- PP-TP53-wt2 PP-TP53- DP-1 DP-2 DP-3 DP-4 wt1 G12C P190S 39-79 P-KRAS-c12/13 P-ACTB PP-KRAS- PP-KRAS- PP-KRAS- PP-KRAS- DP-1 DP-2 DP-3 wt1 G12S G12R G12C PP-KRAS- PP-KRAS- PP-KRAS- PP-KRAS- wt2 G12D G12V G12A PP-KRAS- PP-KRAS- PP-ACTB wt3 G13D Cell lines ONCO- P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 DG-1 II wt2 G12A A427 P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 II wt2 G12D SW480 P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 II wt2 G12V HCT-15 P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 II wt3 G13D A549 P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 II wt1 G12S HUPT3 P-KRAS-c12/13- P-ACTB-II PP-KRAS- PP-KRAS- PP-ACTB DP-1 DP-2 DP-3 II wt1 G12R

TABLE 7 EGFR mutations and prevalence based on cases in the COSMIC database. # Mutation Prevalence 1 L858R 1258 45.48084% 2 2335_2349del15 560 20.24584% 3 2336_2350del15 314 11.35213% 4 2340_2357del18 110 3.97686% 5 T790M 104 3.75994% 6 2339_2348TTAAGAGAAG > C 71 2.56688% 7 2337_2355 > T 43 1.55459% 8 2340_2354del15 41 1.48228% 9 L861Q 34 1.22921% 10 2339_2356del18 28 1.01229% 11 G719S 24 0.86768% 12 G719A 23 0.83153% 13 S768I 22 0.79537% 14 2339_2351 > C 19 0.68691% 15 2337_2351del15 18 0.65076% 16 2339_2347del9 18 0.65076% 17 2339_2353del15 18 0.65076% 18 G719C 16 0.57845% 19 2307_2308ins9 8 0.28923% 20 2339_2358 > CA 7 0.25307% 21 2340_2351del12 7 0.25307% 22 2310_2311insGGT 4 0.14461% 23 2337_2354del18 4 0.14461% 24 2338_2355del18 4 0.14461% 25 2338_2348 > GC 4 0.14461% 26 2319_2320insCAC 2 0.07231% 27 2335_2352 > AAT 2 0.07231% 28 2338_2352 > GCA 2 0.07231% 29 2336_2353del18 1 0.03615%

J. Examples

Embodiments will now be further described with reference to the following non-limiting Examples. It should be understood that these Examples, while indicating embodiments, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Thus, various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. All documents referenced herein are incorporated by reference.

Materials and Methods

Cell Culture:

The cell lines GM08402 (Coriell Cell Repositories) and BJhTERT were cultured in MEM without phenol red and 1-glutamine (Gibco) supplemented with 10% FBS (Sigma), 1× nonessential amino acids (Gibco), 2 mM 1-glutamine (Sigma) and 1× penicillin-streptomycin (PEST, Sigma). Mouse embryonic fibroblasts (MEF) were cultured in DMEM without phenol red and 1-glutamine (Gibco) supplemented with 10% FBS, 2 mM 1-glutamine and 1×PEST. ONCO-DG-1, SW-480, A-427 and HCT-15 (all four from DSMZ), SKOV3 and SKBR3 were cultured in RPMI culture medium (Sigma) supplemented with 10% FBS, 2 mM 1-glutamine and 1×PEST. A-549 (DSMZ) was cultured in DMEM without phenol red and L-Glutamine (Gibco) supplemented with 10% FBS, 2 mM L-Glutamine and 1×PEST. HUP-T3 (DSMZ) was cultured in MEM-Eagle culture medium (Sigma) supplemented with 10% FBS, 2 mM L-glutamine and 1×PEST.

Preparation of Tissue Sections:

Fresh frozen 9-μm sections of E14.5 mouse embryos were placed on Superfrost Plus Gold slides (Thermo Scientific). Fully anonymized fresh frozen human tissue sections from a HER2-positive breast cancer were obtained from the Fresh Tissue Biobank at the Department of Pathology, Uppsala University Hospital, in accordance with the Swedish Biobank Legislation. Breast tissue sections of 4 μm thickness were placed on Starfrost microscope slides (Instrumedics).

Sample Pretreatment for In Situ Experiments:

Cells were seeded on Superfrost Plus slides (Thermo Scientific) and allowed to attach. When the cells reached the desired confluency they were fixed in 3% (w/v) paraformaldehyde (Sigma) in PBS for 30 min at room temperature (20-23° C.). After fixation, slides were washed twice in DEPC-treated PBS (DEPC-PBS) and dehydrated through a series of 70%, 85% and 99.5% ethanol for 3 min each. The molecular reactions were performed in Secure-seals (Grace Bio-Labs, 9 mm in diameter and 0.8 mm deep) attached to the slides. A 50-μl reaction volume was used for each sample. To make the RNA more readily available for cDNA synthesis, 0.1 M HCl was applied to the cells for 10 min at room temperature. This was followed by two brief washes in DEPC-PBS. Tissues were treated similarly to cell lines, with a few exceptions. Tissue fixation was performed in 2% (w/v) paraformaldehyde in PBS. The tissue was then permeabilized with 0.01% pepsin (Sigma) in 0.1 M HCl at 37° C. for 2 min. Molecular reactions were carried out with a reaction volume of 100 μl in Secure-seals (13 mm in diameter, 0.8 mm deep; Grace Bio-Labs) mounted over the tissue. Reverse transcription was carried out overnight and incubation times for ligation, RCA and detection probe hybridization were doubled. For the mouse tissue, ligation was carried out with T4 DNA ligase.

Oligonucleotide Sequences:

Oligonucleotide sequences (Tables 1-3) were designed using GenBank accession numbers NM_001101.3 (ACTB), NM_007393.3 (Actb), NM_198253.2 (TERT), NM_002467 (MYC), NM_001005862.1 (ERBB2), NM_009606 (Acta1), NM_009609 (Actg1) and NM_033360 (KRAS). All padlock probes were 5′-phosphorylated at a concentration of 2 μM with 0.2 U μl⁻¹ T4 polynucleotide kinase (Fermentas) in the manufacturer's buffer A plus 1 mM ATP for 30 min at 37° C., followed by 10 min at 65° C. For β-actin transcript detection in cultured cells, primer P-βe1 was used for detection with padlock probe PLP-βe1, primer P-βe6 with padlock probe PLP-βe6, primer P-βhum with padlock probe PLP-βhum and primer P-βmus with padlock probe PLP-βmus unless otherwise indicated. TERT was detected with primer P-TERT and padlock probe PLP-TERT, cMyc with primer P-cMyc and padlock probe PLP-cMyc and HER2 with primer P-HER2 and padlock probe PLP-HER2. For detection of transcripts in mouse tissue, primer P-βmus was used with padlock probe PLP-βmus for β-actin, primer P-α1mus with padlock probe PLP-α1mus for α1-actin and primer P-γ1mus with padlock probe PLP-γ1mus for γ1-actin. For KRAS genotyping, primer P-KRAS was used in combination with the padlock probes PLP-KRAS-wtGGT, PLP-KRAS-mutGTT and PLP-KRAS-mutGAT.

Sample Preparation for KRAS Genotyping Experiments:

Cell lines ONCO-DG-1, A-427, SW-480, HCT-15, A-549 and HUP-T3 (all DSMZ) were seeded on Collagen I 8-well CultureSlides (BD BioCoat), and allowed to attach. When the cells reached the desired confluency they were fixed in 3% (w/v) paraformaldehyde (Sigma) in DEPC-treated PBS (DEPC-PBS) for 30 min at room temperature (20-23° C.). After fixation slides were washed twice in DEPC-PBS and the plastic wells were removed from the slides. The slides were thereafter dehydrated through an ethanol series of 70%, 85% and 99.5% ethanol for 1 min each.

Fresh frozen and FFPE human tumor tissues from colorectal- and lung cancer patients were obtained from the Biobank at the Department of Pathology and Cytology (Botling and Micke, 2011), Uppsala University Hospital, in accordance with the Swedish Biobank Legislation and Ethical Review Act (Uppsala Ethical Review Board approval, reference numbers 2006/325 and 2009/224).

Tape transferred fresh frozen tissue sections (4 μm) on Starfrost microscope slides (Instrumedics) were prepared from fresh frozen tumor samples stored at −80° C. The slides were fixed in 3% (w/v) paraformaldehyde in DEPC-PBS for 45 min at room temperature and then permeabilized with 0.01% pepsin (Sigma, #P0609) in 0.1 M HCl at 37° C. for 2 min followed by a brief wash in DEPC-PBS.

Touch imprints, prepared on Superfrost Plus microscope slides, were obtained from fresh surgical colorectal and lung cancer specimens. After slide preparation the slides were air-dried for 1 min and thereafter stored at −80° C. The slides were fixed in 3% (w/v) paraformaldehyde in DEPC-PBS for 30 min at room temperature followed by a brief wash in DEPC-PBS.

FFPE tissue sections (4 μm) were placed on Superfrost Plus microscope slides (Menzel Gläser and baked for 30 min at 60° C. The slides were then deparaffinized by immersion in xylene for 15+10 min and thereafter gradually rehydrated through an ethanol series (2×2 min in 100%, 2×2 min in 95%, 2×2 min in 70%, and finally for 5 min in DEPC-H₂O). The slides were washed in DEPC-PBS for 2 min before fixation with 4% (w/v) paraformaldehyde in DEPC-PBS for 10 min at room temperature which was followed by another DEPC-PBS wash for 2 min. The FFPE tissue slides were then permeabilized in 2 mg ml-1 Pepsin (Sigma #P7012) in 0.1 M HCl at 37° C. for 10 min. The digestion was stopped by a wash in DEPC-treated H₂O (DEPC-H₂O) for 5 min followed by a wash in DEPC-PBS for 2 min. Finally, the slides were fixed a second time with 4% (w/v) paraformaldehyde in DEPC-PBS for 10 min at room temperature and washed in DEPC-PBS for 2 min. After completed pretreatments of tissues, the slides were dehydrated through an ethanol series of 70%, 85% and 99.5% ethanol for 1 min each.

The KRAS mutation status of the tissues was analyzed by Pyrosequencing (Pyromark Q24 KRAS, Qiagen GmbH, Hilden, Germany) as described previously (Sundstrom et al., 2010).

In Situ cDNA Detection Procedure:

Samples were preincubated in M-MuLV reaction buffer. Then 1 μM of cDNA primer was added to the slides with 20 U μl⁻¹ of RevertAid H minus M-MuLV reverse transcriptase (Fermentas), 500 nM dNTPs (Fermentas), 0.2 μg μl⁻¹ BSA (NEB) and 1 U μl⁻¹ RiboLock RNase Inhibitor (Fermentas) in the M-MuLV reaction buffer. Slides were incubated for 3 h to overnight at 37° C. After incubation, slides were washed briefly in PBS-T (DEPC-PBS with 0.05% Tween-20 (Sigma)), followed by a postfixation step in 3% (w/v) paraformaldehyde in DEPC-PBS for 30 min at room temperature. After postfixation, the samples were washed twice in PBS-T. To make the target cDNA strands available for padlock probe hybridization, the RNA portion of the created RNA-DNA hybrids was degraded with ribonuclease H. This was performed in the same step as the padlock probe hybridization and ligation. For most reactions, Ampligase (Epicentre) was used for ligation. Samples were first preincubated in Ampligase buffer (20 mM Tris-HCl, pH 8.3, 25 mM KCl, 10 mM MgCl₂, 0.5 mM NAD and 0.01% Triton X-100). Ligation was then carried out with 100 nM of each padlock probe in a mix of 0.5 U μl⁻¹ Ampligase, 0.4 U μl⁻¹ RNase H (Fermentas), 1 U μl⁻¹ RiboLock RNase Inhibitor, Ampligase buffer, 50 mM KCl and 20% formamide. Incubation was performed first at 37° C. for 30 min, followed by 45 min at 45° C. For detection of actin transcript isoforms in mouse embryonic tissue sections, ligation was instead carried out using T4 DNA ligase (Fermentas). Samples were then first preincubated in T4 DNA ligase buffer (Fermentas). Then 100 nM of each padlock probe was added with 0.1 U μl⁻¹ T4 DNA ligase, 0.4 U μl⁻¹ RNase H, 1 U μl⁻¹ RiboLock RNase Inhibitor and 0.2 μg μl⁻¹ BSA in T4 DNA ligase buffer supplemented with 0.5 mM ATP and 250 mM NaCl. Slides were then incubated at 37° C. for 30 min. After ligation with Ampligase or T4 DNA ligase, slides were washed in DEPC-treated 2×SSC with 0.05% Tween-20 at 37° C. for 5 min and rinsed in PBS-T. Slides were preincubated briefly in Φ29 DNA polymerase buffer (Fermentas). RCA was then performed with 1 U μl⁻¹ Φ29 DNA polymerase (Fermentas) in the supplied reaction buffer, 1 U μl⁻¹ RiboLock RNase Inhibitor, 250 μM dNTPs, 0.2 μg μl⁻¹ BSA and 5% glycerol. Incubation was carried out for 60 min at 37° C. The incubation was followed by a wash in PBS-T. RCPs were visualized using 100 nM of each corresponding detection probe in 2×SSC and 20% formamide at 37° C. for 30 min. Slides were then washed in PBS-T, the Secure-seals were removed and the slides were dehydrated using a series of 70%, 85% and 99.5% ethanol for 3 min each. The dry slides were mounted with Vectashield (Vector), containing 100 ng ml⁻¹ DAPI to counterstain the cell nuclei. The protocol for counterstaining of cell membranes in FIG. 5 is described under “WGA Staining” below.

WGA Staining:

For counterstaining of cytoplasms 2.5 μg ml⁻¹ WGA 488 (Invitrogen) diluted in 1×PBS was added for 60 min at room temperature. This was followed by two washes in PBS-T and dehydration before mounting and nuclear staining with DAPI as described before.

Single-Cell Quantification:

For single-cell quantification in FIG. 6, a custom made MatLab script was used for marking individual cells and counting RCPs within the marked areas. The quantification of RCPs in MatLab differs in how an RCP is defined compared to the BlobFinder software used for quantification in other Examples herein. As a consequence the results show ˜30% fewer RCPs compared to the BlobFinder analysis.

Image Acquisition and Analysis:

Images of cultured cells were acquired using an Axioplan II epifluorescence microscope (Zeiss) equipped with a 100 W mercury lamp, a CCD camera (C4742-95, Hamamatsu), and a computer-controlled filter wheel with excitation and emission filters for visualization of DAPI, FITC, Cy3, Cy3.5 and Cy5. A ×20 (Plan-Apocromat, Zeiss), ×40 (Plan-Neofluar, Zeiss) or ×63 (Plan-Neofluar, Zeiss) objective was used for capturing the images. Images were collected using the Axiovision software (release 4.3, Zeiss). Exposure times for cell images were 260-340 ms (at ×20 magnification), 10-80 ms (×40) or 220 ms (×63) for DAPI; 40 ms (×40) or 220 ms (×63) for FITC; 560-640 ms (×20), 110-160 ms (×40) or 200 ms (×63) for Cy3; 110 ms (×40) or 250 ms (×63) for Texas Red; and 6,350 ms (×20), 180 ms (×40) or 350 ms (×63) for Cy5. For SKBR3 and SKOV3 cells, images were collected as z-stacks to ensure that all RCPs were imaged. The imaging of α1-actin and β-actin in fresh frozen mouse embryonic tissue sections in Example 3 was imaged using a Mirax Midi slide scanner (3D Histech) equipped with a CCD camera (AxioCam MRm, Zeiss) and a ×20 Plan-Apochromat objective. Exposure times in the slide scanner were 45 ms for DAPI, 270 ms for Cy3, 340 ms for Texas Red and 3,200 ms for Cy5. For quantification, the numbers of RCPs and cell nuclei in images were counted digitally using BlobFinder software (version 3.0_beta). For cultured cells, the quantification was done on five 20× microscope images (approximately 20-30 cells for each sample). The total number of RCPs was divided by the number of nuclei for each image. The average for each sample was then calculated from the result of the five images and is reported as RCPs per cell. The procedure for single-cell quantification used in FIG. 6 is described “Single cell quantification” above.

qPCR for β-Actin Transcript Quantification in Cells:

Two separate passages of the cell line GM08402 were collected after counting of cells, and total RNA was purified from the cells using the PARIS kit (Ambion) with the protocol for RNA isolation from total cell lysate. Traces of DNA were removed from the purified RNA using the DNA-free kit (Ambion). First-strand cDNA synthesis was carried out with 700 ng of template RNA in a mix containing 20 U RevertAid H minus M-MuLV reverse transcriptase (Fermentas) in the corresponding enzyme buffer, 0.5 μg oligo(dT) primer (20-mer), 1 mM dNTPs and 1 U μl⁻¹ RiboLock RNase Inhibitor. Samples were incubated at 37° C. for 5 min, followed by 42° C. for 60 min. The reaction was stopped by heating to 70° C. for 10 min. A preparative PCR was carried out to synthesize template for standard curve creation. For this PCR, 1 μl of cDNA from one of the cell passages was amplified in a mix of 0.02 U μl⁻¹ Platinum Taq DNA polymerase (Invitrogen), PCR buffer, 2 mM MgCl₂, 200 μM dNTPs, 200 nM ACTBfwd primer and 200 nM ACTBrev primer in a total volume of 50 μl. PCR was carried out with 2 min at 95° C., followed by cycling 45 times (95° C. for 15 s, 50° C. for 15 s, and 72° C. for 1 min) and finishing with 72° C. for 5 min. The PCR product was purified using the Illustra GFX PCR and gel band purification kit (GE Healthcare) according to the protocol for purification of DNA from solution. The concentration of the purified PCR product was measured using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and the number of molecules per microliter was calculated. qPCR was run with 2 μl of template cDNA, or diluted standard curve PCR product, with SYBR Green (Invitrogen), 0.02 U μl⁻¹ Platinum Taq DNA polymerase, PCR buffer, 2 mM MgCl₂, 200 μM dNTPs, 200 nM ACTBfwd primer and 200 nM ACTBrev primer in a total volume of 30 μl. The qPCR was run using the same program as for the preparative PCR. Standard curve samples were run in duplicates of the same sample and cDNA samples from the two passages of cells were run in triplicates. Calculations of transcript copy numbers for the two cell passages were based on the number of counted cells at harvest. The average β-actin mRNA copy number for the cell line was then determined. The protocol for efficiency estimation by qPCR for the in situ multiplex detection experiment is as follows:

The cell lines GM08402, SKBR3 and BJhTERT were harvested after counting of cells and total RNA was purified from the cells using the RiboPure kit (Ambion). DNA traces were removed from the purified RNA using the DNA-free kit (Ambion). RNA concentration and quality was investigated on an Agilent Bioanalyzer using a RNA 6000 Pico chip (Agilent). First strand cDNA synthesis was carried out using the High capacity cDNA reverse transcription kit (Applied Biosystems). The prepared cDNA was diluted 4× before analysis with TaqMan qPCR. PCR primers and TaqMan probes were purchased as validated 20× TaqMan Gene Expression Assays from Applied Biosystems (assay no Hs99999903_m1 for β-actin, Hs00972650_m1 for TERT, and Hs99999005_mH for HER2). Templates for standard curves for the different genes were created by PCR. For this PCR, 1 μl of cDNA from the BJhTERT cell line was amplified in a mix of 0.02 U μl⁻¹ Platinum Taq DNA polymerase (Invitrogen), 1×PCR buffer, 2 mM MgCl2, 200 μM dNTP, and 0.01× of each primer mix (0.2 μM of each primer) in separate reactions for the different genes. The total PCR volume was 50 μl and the PCR was carried out with 2 min at 95° C., followed by cycling 45× (95° C. for 15 s and 60° C. for 1 min), and finished with 60° C. for 5 min. The PCR products were purified using the Illustra GFX PCR and gel band purification kit (GE Healthcare). The concentration of the purified PCR products was measured using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and the number of molecules per μl was calculated. The qPCR was run with 4 μl of template cDNA, or standard curve PCR product in 1× TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems) with 1× TaqMan Gene Expression Assay primer and probe mix in a total volume of 20 μl. The qPCR program was run with 10 min at 95° C., followed by cycling 40× with 95° C. for 15 s and 60° C. for 1 min. All samples were run in duplicates and featured serial dilutions of the standard curves, serial diluted cDNA samples, RNA controls from the cell lines, and no template controls. Calculations of transcript copy numbers were based on the number of counted cells at harvest.

In Situ Genotyping of KRAS on Cell Lines and Tissues:

All the molecular in situ reactions were carried out in Secure-seals (Grace Bio-Labs Inc.) and the reaction volumes for tissues or imprints were either 100 μl (size 13 mm diameter, 0.8 mm deep) or 350 μl (size 22 mm diameter, 0.8 mm deep) depending on the size of the sample. The Secure-seals that were used for cells had a total volume of 50 μl (size 9 mm diameter and 0.8 mm deep). The Secure-Seals were mounted over the cells or tissues and the wells were dehydrated by a brief flush with PBS-T (DEPC-PBS with 0.05% Tween-20 (Sigma)).

The samples were thereafter treated in the same way with just the following exceptions. Post-fixation of fresh frozen and FFPE tissues was performed for 45 min compared to 30 min for cell lines imprints. Also, the RCA time on tissues was longer (8 h) compared to cultured cells and tumor imprints (2 h). For all reactions slides were incubated in humid chambers.

Oligonucleotide Sequences for KRAS Genotyping Experiments:

Oligonucleotides sequences (Table 4) were designed using GenBank accession numbers NM_033360 (KRAS), NM_005228 (EGFR), NM_001126114.1 (TP53) and NM_001101.3 (ACTB). All padlock probes were 5′ phosphorylated at a concentration of 10 μM with 0.2 U μl⁻¹ T4 PNK (Fermentas) in PNK buffer A and 1 mM ATP for 30 min at 37° C., followed by 10 min at 65° C. The primers, padlock probes and detection probes applied on the different tissue samples and cell lines are summarized in Table 6.

One μM of cDNA primer was added to the slides with 20 U μl⁻¹ of RevertAid H minus M-MuLV reverse transcriptase (Fermentas), 500 μM dNTP (Fermentas), 0.2 μg μl⁻¹ BSA (NEB), and 1 U μl⁻¹ RiboLock RNase Inhibitor (Fermentas) in the M-MuLV reaction buffer. Slides were incubated for 3 hours at 37° C.

After incubation slides were washed briefly by flushing the wells in PBS-T, followed by a post-fixation step in 3% paraformaldehyde (w/v) in DEPC-PBS for 45 (fresh frozen and FFPE tissues) or 30 (imprints) minutes at room temperature. After post-fixation the samples were washed by flushing the Secure-seals chambers with PBS-T.

RNase H Digestion, Padlock Probe Hybridization and Ligation for KRAS Genotyping Experiments:

To create single-stranded target cDNA available for padlock probe hybridization, the RNA part of the created RNA-DNA hybrids was degraded with RNase H. This was performed in the same step as hybridization and ligation of the padlock probes. The reaction was carried out with 100 nM of each padlock probe in a mix of 1 U μl⁻¹ Ampligase (Epicentre), 0.4 U μl⁻¹ RNase H (Fermentas), 1 U μl⁻¹ RiboLock RNase Inhibitor, 50 mM KCl, 20% formamide in Ampligase buffer. Incubation was performed first at 37° C. for 30 min, followed by 45 min at 45° C. After ligation, slides were washed flushing the chambers with PBS-T. For prospective KRAS mutation detection of unknown tissue samples a cocktail of all KRAS codon 12 and 13 padlock probes was mixed with a final concentration of 10 nM.

Amplification and Detection of Circularized Padlock Probes for KRAS Genotyping Experiments:

RCA was performed with 1 U μl⁻¹ Φ29 DNA polymerase (Fermentas) in the supplied reaction buffer with 1 U μl⁻¹ RiboLock RNase Inhibitor, 250 μM dNTP, 0.2 μg μl⁻¹ BSA, and 5% glycerol. Incubation was carried out for 2 h for tumor imprints as well as for cell lines and approximately 5 h for fresh frozen and FFPE tissues at 37° C. After RCA the samples were washed flushing the Secure-seals chambers with PBS-T. RCPs were visualized using 100 nM of each corresponding detection probe in 2×SSC and 20% formamide at 37° C. for 15 mM. Slides were then washed again by flushing the chambers in PBS-T, the Secure-seals were removed and the slides were dehydrated using a series of 70%, 85%, and 99.5% ethanol for 30 sec each. The dry slides were mounted with Vectashield (Vector), containing 100 ng ml⁻¹ DAPI to counterstain the cell nuclei.

Image Acquisition and Analysis for KRAS Genotyping Experiments:

Images were acquired using an AxioplanII epifluorescence microscope (Zeiss), equipped with a 100 W mercury lamp, a CCD camera (C4742-95, Hamamatsu), and a computer-controlled filter wheel with excitation and emission filters for visualization of DAPI, FITC, Cy3 and Cy5. For capturing the images, a ×10 (Plan-Apocromat, Zeiss) objective was used for fresh frozen and FFPE tissues, a ×20 (Plan-Apocromat, Zeiss) objective for tumor imprints and finally a ×63 (Plan-neofluar, Zeiss) objective was used for the cells. Images were collected using the Axiovision software (Release 4.8, Zeiss). Images displayed for illustrations were processed using image editing software for clarity in print. The threshold for different color channels was set using ImageJ 1.42q and for clearer visualization of the KRAS signals in Cy3 and Cy5, a maximum filter was applied.

Example 1 Detection of β-Actin (ACTB) Transcripts in Cultured Human Cells Using Padlock Probes

To detect β-actin (ACTB) transcripts in cultured human cells, two different padlock probes were used targeting sequences in the first and last exon, respectively. Many bright, spot-like signals localized to the cytoplasm of cells were visualized, consistent with previous observations of this transcript consistent with previous reports regarding this transcript. The detection efficiency was similar for the two padlock probes, indicating that in this case detection was not highly dependent on target position along the transcript (FIG. 5). In contrast, when reverse transcriptase was omitted from the cDNA synthesis reaction, no signals were detected, verifying that the signals were cDNA dependent (FIG. 5). It was estimated that the overall in situ detection efficiency to be ˜30% of available transcripts, on the basis of a comparison to quantitative PCR (qPCR) data for β-actin mRNA in the GM08402 cell line (2,000 copies per cell). There was considerable variation in the number of signals among cells (FIG. 6), consistent with other reports of intercellular variation in β-actin mRNA expression.

Example 2 Detection of Single-Nucleotide Variants of Transcripts in Cultured Cells In Situ

To demonstrate high selectivity of detection, an assay was used to detect of single-nucleotide variants of transcripts in situ. Expressed polymorphisms are rare in β-actin, therefore a single-base difference between the human and mouse β-actin sequences was used as genotyping target. Co-cultured human and mouse fibroblast cells were subjected to in situ genotyping of cDNA using padlock probes PLP-Phum (human) and PLP-βmus (Mus musculus) and target-primed RCA. There was a clear-cut distinction observed between the two subpopulations of cells in the co-culture. The preference for perfectly matched padlock probes at the circularization step ensures distinction between the two targets by the ligase.

Example 3 Detection of Single-Nucleotide Variants of Transcripts in Fresh Frozen Tissue In Situ

To test the method in fixed tissue sections, closely related skeletal muscle α1-actin (Acta1) and cytoplasmic β-actin (Actb) transcripts were targeted in fresh frozen tissue from an E14.5 mouse embryo cross sectioned at the level of the neck. The two actin transcripts were successfully detected in the tissue using padlock probes designed with target sequences differing by a single base. The α1-actin signals were mainly distributed to skeletal muscles, whereas β-actin signals were widely distributed but showed slightly more signals in the non-muscular tissue. The ability to distinguish three transcripts from the same gene family was demonstrated by including a probe specific for the cytoplasmic α1-actin (Acta1) transcript.

Example 4 Detection of Transcripts for Expression Profiling

To test the method's ability for multiplex detection of transcripts for expression profiling, padlock probes were designed for the three cancer-related transcripts HER2 (also known as ERBB2), cMyc (also known as MYC) and TERT. Using β-actin as a reference transcript, these transcripts were assayed in four cell lines (a human ovarian carcinoma cell line, a human breast carcinoma cell line, a TERT-immortalized human foreskin fibroblast cell line and a primary fibroblast cell culture). The levels of expression of the cancer-related genes differed among the cell lines (FIG. 2a-d ). The ovarian and breast carcinoma cell lines showed similar patterns of expression of the HER2 and cMyc transcripts, whereas the TERT-immortalized fibroblast was the only cell type with a detectable level of the TERT transcript. All four cell lines expressed β-actin, and in the normal fibroblasts this was the only investigated transcript expressed at a detectable level. These results were compared to qPCR data and to available literature and good correlation with the expected relative expression levels in the different cell lines and a notable consistency in detection efficiency among the different transcripts was found (Example 5). Large cell-to-cell variation in expression for all investigated transcripts was noticed, which is consistent with previous studies of expression in single cells in cultures.

Example 5 Expression of Cancer-Related Transcripts in Human Cell Lines

The three cancer-related transcripts TERT, HER2, and cMyc were assayed in four cell lines as described in Example 4. All cell lines expressed the housekeeping gene β-actin, but differed in the expression of the cancer-related transcripts according to the in situ data. qPCR measurements were then performed to quantify the different transcripts in the GM08402, BJhTERT and SKBR3 cell lines to be able to evaluate the variation in detection efficiency in the in situ experiments. qPCR measurements of TERT expression showed relatively high expression in the BJhTERT cell line (247 molecules/cell), as well as low expression in the SKBR3 breast carcinoma cell line (6 molecules/cell). No TERT expression was detected in the normal primary fibroblasts by qPCR. The qPCR data for TERT correlates well with the mRNA expression level for TERT found in the literature (220 molecules/cell for BJhTERT and 0.57 molecules/cell for SKBR3 (Yi et al., 2001). The in situ result of 39 RCPs detected per cell in BJhTERT thus corresponds to a detection efficiency of 16% based on the qPCR data. The HER2 transcript is known to be overexpressed in the ovarian and breast carcinoma cell lines. In the SKBR3 cell line the number of HER2 mRNAs/cell is reported to be 168-336 molecules, the qPCR measurement described herein ended at 177 molecules/cell. The number of HER2 mRNAs/cell detected in situ was 25. This gives a detection efficiency of 14% for the HER2-transcript in SKBR3 cells. HER2 expression could not be detected by qPCR in the normal primary fibroblasts or in the BJhTERT cell line. The expression level of cMyc in SKOV3 cells is estimated to about one quarter of the number of HER2 transcripts in the same cell line, which correlates well with the in situ measurement described herein. When assayed alone, the detection efficiency for β-actin in cultured fibroblast cells was estimated to be 30% based on qPCR measurements and in situ detection of the transcript. In these multiplex experiments the detection efficiency is slightly lower, about 15%, based on the same qPCR estimation. A similar effect is observed among the cancer transcripts that show detection efficiencies of about 15% in multiplex, while they perform better individually. It is likely that the lower detection efficiency observed for targets in multiplex experiments are due to interactions between different padlock probes and/or cDNA primers, especially since the LNA modified bases of the cDNA primers have the capacity to bind very strongly to each other. The detection protocol for multiplex reactions can be improved by optimizing the concentration of the probes and/or primers. Further qPCR measurements show good correlation with the in situ measurements for the relative β-actin expression level between the cell lines. Taken together these data indicate that the relative levels of RCPs in the different cell types are good estimates of the true relative transcript levels in the cell populations. Thus it is believed that the method is suitable for relative expression profiling in different samples. Although as the reverse transcription reaction is known to introduce variation in mRNA quantification by qPCR, this is likely to be the case also for reverse transcription in situ.

Example 6 Detection of Transcript Distribution in a Fresh Frozen HER2-Positive Human Breast Cancer Tissue

The technique of this embodiments was also used to assess HER2 transcript distribution in a fresh frozen HER2-positive human breast cancer tissue section. Expression varied widely among the cells, consistent with the expected presence of cancer cells and normal stroma in the tumor tissue.

Example 7 Genotyping of a KRAS Point Mutation in KRAS Wild-Type and Mutant Cells

The method of the embodiment was also used to genotype a KRAS point mutation in KRAS wild-type and mutant cells (FIG. 7). The different cell types could be clearly distinguished on the basis of the color of their corresponding RCPs. Activating mutations of the KRAS oncogene are found in 17%-25% of all human tumors, and assays to monitor these mutations and other tumor cell-specific markers in tissue specimens in situ could be of great value for clinical pathology investigations. The potential for studies of allelic expression was further investigated by analyzing 77 cells from a cell line heterozygous for a point mutation in KRAS. An average allelic ratio of 48% wild-type transcripts was observed, with considerable cell-to-cell variation (FIGS. 6b and 7), indicating a balanced allelic transcription. In this experiment, all heterozygous cells with more than seven RCPs showed signals from both alleles. For cells showing fewer than seven signals, it will be difficult to determine the potential for biallelic expression and extent of unbalanced allelic expression in single cells.

Example 8 Effect of LNA Base Incorporation in the cDNA Primer

To increase the efficiency of the reverse transcription step, a RT primer with incorporated locked nucleic acid (LNA)-bases was used. LNA modified oligonucleotides have previously been used for FISH, with DNA/LNA mixmers with every second or third base substituted for LNA performing the best. In addition to the increased hybridization efficiency to the targets, the LNA content of the primers can be designed to protect the target RNA from breakdown by RNase H. This means that in the present method, the in situ synthesized cDNA can maintain the localization to the detected mRNA molecule in the cell via the hybridization of the cDNA primer (FIG. 1). cDNA primers with different LNA substitutions (Table 2) were tested in situ for subsequent detection of the PLP-βe1 padlock probe target site. It was found that primers with every second base at the 5′-end substituted with LNA performed better than primers with substitutions of every third base (FIG. 3). Primers with five, seven or nine LNA bases in total were also investigated and it was found that adding nine LNA bases resulted in a small decrease in the amount of signals in situ. To ensure that the LNA would not interfere with the ability of the reverse transcriptase to synthesize cDNA from the primer, LNA bases were placed on the 5′-side of the primers, leaving the 3′-end unmodified. It was found that shortening the total length of the primer from 30 to 25 nucleotides did not influence the results, and thus it was concluded that the priming is not disturbed by the presence of LNA bases in the primer.

Example 9 cDNA Synthesis Efficiency

To ensure an optimal distance between hybridizing cDNA primers and target sequences for the padlock probes, the length of the produced cDNA molecules in cells was investigated. An in situ detection experiment was set with cDNA primers located at different distances from the 5′-end of the β-actin mRNA. Reverse transcription was then performed in situ and the resulting cDNA molecules were detected with PLP-βe1, with a target sequence near the 3′-end of the reverse transcribed cDNA. The number of RCPs formed per cell was then quantified for the different primers. The primers tested were to result in cDNA molecules ranging from approximately 90-500 nt in length, measured from the start of the primer site to the end of the transcript (see Table 3 for primer sequences). It was found that predominantly short molecules were formed and that the cDNA primer site should be located close to the padlock probe target site (FIG. 4). As well as providing details on how to design primers for reverse transcription, the knowledge about the limited cDNA synthesis length has a practical relevance for the execution of the RCA reaction. In this protocol a target-priming strategy was used that was originally described for endogenous mitochondrial DNA molecules in situ (Larsson et al., 2004). Target-priming takes advantage of a 3′-5′ exonuclease activity of the φ29 DNA polymerase on single stranded DNA to create a primer from a nearby 3′-end of the target molecule. The efficiency of the RCA reaction has been shown to decrease as the length of the protruding 3′-end of mitochondrial DNA is increased from 0 to 130 nucleotides. As very short cDNA molecules were produced in this method, the target-primed RCA approach can efficiently be applied for signal amplification also for cDNA detection without further preparation of the target strand.

Example 10 Different Ligases for Ligation of Padlock Probes

There are mainly two enzymes that have been used for padlock probe ligation previously; the ATP dependent T4 DNA ligase and the NAD+ dependent Ampligase™. Both ligases were tested for in situ detection of cDNA with padlock probes, good detection efficiencies were obtained. However, when performing the experiments for detection of sequences with single nucleotide resolution in human and mouse cells, it was found that Ampligase resulted in a lower proportion of signals from the non-matched probe. The proportion of correct signals with T4 DNA ligase was 87% (human RCPs/total RCPs) for human cells and 98% (mouse RCPs/total RCPs) for mouse cells. This is in contrast to Ampligase™, which had a much higher selectivity for the human target sequence (98% correct) whereas the mouse target sequence was unchanged compared to T4 DNA ligase. As the transcripts of the different actin isoforms share a high proportion of similarity and many pseudogenes exist, it is believed that some of these unexpected positive signals originate from sequences similar to the padlock probe target sequence that do not show up when performing simple in silico sequence analysis. In addition to these observations, Ampligase™ is known to be more specific for matched substrates than T4 DNA ligase.

Example 11 Assay Design for In Situ Mutation Detection

Padlock probes were designed for point mutations of KRAS in codon 12 and 13 (G12S, G12R, G12C, G12D, G12A, G12V and G13D) and codon 61 (Q61H), as well as for EGFR (G719A, G719C, S768I and L858R) and TP53 (S127F and P190S). Padlock probes for the wild-type forms of the different targets were designed as well. The mutation-specific padlock probes were designed with identical target sequences except for the last nucleotide in the 3′-end that differ depending on genotype. Mismatches at this position are not accepted by the DNA ligase used and single nucleotide differences, like point mutations, are therefore efficiently discriminated. There are furthermore two different sites for detection probes for wild-type and mutant padlocks to distinguish the RCPs from each other using detection probes labeled with different fluorescence dyes, e.g. green and red. Also detection of the ACTB transcript was included in these assays, detected by an additional fluorophore, as an internal reference having a relative constant expression between cell types. A comparison of the ACTB signals across samples provided an estimation of the detection efficiency in different samples. The ACTB data has been useful during the development phase of this study, but turned out to be dispensable for mutation scoring and tissue classification.

Example 12 Mutation Detection in Fresh Frozen Colon and Lung Tissues with Known KRAS Status

The selectivity of the padlock probes was first tested in situ on wild-type- and mutation-specific KRAS cell lines. After confirmation of the quality of the probes, our in situ genotyping method was applied on ten fresh frozen human colon and lung cancer tissues with known KRAS status. In this validation phase, each probe-pair (one probe for a particular mutation and one for the corresponding wild-type variant) was tested individually on a collection of fresh-frozen tissue samples with known KRAS status. Wild-type probes were designed to generate green fluorescence RCPs and mutation-specific probes to generate red fluorescence RCPs. The samples represented all codon 12 and 13 mutations except for the rarest one, G12R. However, the performance of the padlock probe pair for the G12R mutation was still verified for specificity on one of the tested cell lines. Thus, KRAS wild-type tumor tissues could be distinguished from ones having tumors carrying activating KRAS mutations by microscopic visualization in a fashion similar to regular fluorescent in situ hybridization (FISH). The colon and lung sections with KRAS mutations displayed a mixture of signals originating from both of the probes in the padlock probe pair, whereas the normal tissues showed signals exclusively from the wild-type padlock probe. By visually examining the ten samples variations can clearly be seen in KRAS expression levels both within and between the tissues. Overall, a slightly higher expression level of KRAS was noticed in lung compared to colon. The results showed that most cases displayed both wild-type and mutant KRAS signals in the tumor cell areas indicating heterozygous expression. In contrast, one lung sample almost exclusively displayed mutant signals in the tumor regions while the few existing wild-type signals belonged to the normal surrounding stroma. This could reflect a KRAS homozygous mutation or loss-of-heterozygosity (LOH).

Example 13 Mutation Detection in FFPE Tissue

The in situ padlock probe technique was tested to evaluate whether it could be applicable on FFPE tissue. The protocol applied on this type of tissue material was essentially the same as for fresh frozen tissues, except for the pretreatment procedure. KRAS mutation analysis was performed on a collection of 14 colorectal FFPE cancer tissues with known KRAS mutations in codon 12 and 13 applying the respective padlock probe-pair. All tissues displayed a mixture of signals originating from both the wild-type and mutant padlock probe, however variation in the number of signals (for both KRAS and ACTB) were significant between tissues, which probably reflects the expected difference in tissue quality among FFPE samples. Moreover, the ratio between wild-type and mutant signals was also observed to differ between tissues carrying the same KRAS mutation which probably reflects tumor-specific characteristics. Probes were also designed for the most common mutation in codon 61 (Q61H) and tested in two colon tumor FFPE samples that successfully were scored as mutants.

Example 14 In Situ Detection of KRAS Mutations on Prospective Clinical Samples with Unknown Mutation Status

After the initial verification that the padlock probes are selective, all probes were combined into single reactions that could answer the primary diagnostic question whether a case is KRAS positive or not. This was tested by comparing in situ mutation detection using single pairs of KRAS mutation-specific padlock probes with a multiplex detection approach using a padlock probe cocktail containing all probes for KRAS codon 12 and 13 mutations. The results, based on visual examinations of the tissues, indicated that neither efficiency nor selectivity were lost when multiple probes were in competition for the two-codon target site. The analysis thus provides a rapid answer if the tumor harbors an activating KRAS mutation or not. Nevertheless, if requested there is still a possibility with this technique to reveal the exact sequence alteration by simply testing for all mutations individually on consecutive sections.

Multiplex mutation detection was thereafter demonstrated on eight prospective lung FFPE tissues with unknown KRAS mutations status. Approximately 15-30% of all lung cancer cases have activating KRAS mutations. After performing mutation analysis with padlock probes and RCA, three of the eight cases were concluded to be mutated. The results were compared with pyrosequencing on the same tissues and the suggested genotypes were confirmed to be correct for every case.

To test the method in a diagnostic setting involving cytology preparation tumor imprint slides were prepared from eight prospective fresh colon cancer specimens with unknown KRAS mutation status. Multiplex KRAS mutation detection using padlock probes and target-primed RCA were prepared using the protocol for unfixed tissue. By microscopic examination of the imprints, two cases were found to be positive in the in situ mutation assay, while the other six tumor imprints only showed wild-type signals. DNA from corresponding FFPE tumor sections from the same cases were thereafter tested for KRAS mutations by pyrosequencing. The pyrosequencing results were completely concordant with the in situ assay.

Example 15 High-Throughput Mutation Screening on Tissue Microarrays

Tissue microarrays (TMA) can be used to analyze hundreds of patient FFPE tumor samples on one slide, and have been used to characterize protein expression (by immuno-histochemistry (IHC)) and gene copy number variations (by FISH) in large patient cohorts. Here a TMA containing 25 FFPE colon samples (in duplicates) was assayed for possible KRAS codon 12 and 13 mutations. The array consisted of samples from normal colon mucosa, tubular adenomas, serrated adenomas, primary tumors and matched metastasis, all with unknown mutation status for KRAS. Of all samples eleven were found to be KRAS positive—two adenomas, one serrated adenoma, four primary tumors and their matched metastasis. Mutation analysis by pyrosequencing on the corresponding FFPE blocks was completely concordant with the in situ data (Supplementary FIG. 12).

Example 16 Differential Expression of Mutated Oncogene Alleles Related to Tumor Progression and Histological Heterogeneity

Variable expression of a mutated oncogene across a tumor could potentially result in a variable response to targeted therapy in different areas of a single cancer lesion. Therefore, cases were screened with the in situ assay for distinct patterns of expressed mutations. In one colon cancer case with a codon 61 mutation, the histological progression from normal colon mucosa to low-grade and high-grade dysplasia and invasive carcinoma could be visualized on a single slide. There was a clear increase in the expression of the mutation along with tumor progression. Thus, one can speculate if the level of resistance to EGFR inhibitors would follow the expression levels in the different neoplastic compartments.

Also, the EGFR L858R mutation was targeted in a set of nine FFPE lung tissues in which eight were known to be positive. The results from the in situ mutation assay were completely concordant with the DNA sequencing data. Even though some of the lung samples were collected more than a decade ago high detection efficiency was observed with high numbers of signals, especially mutant signals, which might reflect high mRNA expression from amplified EGFR in the tumor. In one lung sample a great histological heterogeneity was observed with regard to tumor growth patterns. Wild-type EGFR was only expressed in normal bronchial epithelium. In areas with bronchioalveolar/lepidic growth pattern the expression of mutated EGFR was low, and equaled the expression of the wild-type allele. The expression of the mutant allele increased in more poorly differentiated glandular areas, both in absolute numbers and relative to the wild-type allele. The expression of mutant EGFR peaked in areas with solid growth pattern. Thus, if the expression level of L858R affects the sensitivity of a tumor clone for EGFR-TKI therapy, the poorly differentiated areas of the tumor would be expected to respond better than the well differentiated areas in this individual tumor.

Example 17 Expression Patterns in Tumors with Multiple Mutations

To further study intra-tumor heterogeneity, probes were designed for tumors that were known to harbor multiple point mutations. Personalized medicine implies therapy tailored to the individual characteristics of a patient. The advent of next-generation sequencing technology is now increasingly providing researchers, and soon probably clinicians, with mutational profiles of individual tumors that taken together may provide improved opportunities for individualized therapy. Sequencing DNA prepared from a part of a tumor will reveal all mutations in that sample but not if they reside in different sub-clones of the tumor. As a proof-of-concept that intergenic tumor heterogeneity can be studied with our technology, individualized in situ mutation assays were set up for screening of FFPE cases carrying unique combinations of mutations in EGFR, KRAS, and TP53.

One lung cancer case was positive for the activating EGFR mutation G719C as well as the EGFR S768I mutation that is associated with resistance to anti-EGFR therapy. Both mutation variants were successfully detected with the padlock probe-based in situ technique and their individual expression patterns were identified. The expression of the G719C mutation was high compared to the S768I mutation throughout the tumor section. This balance between the expressed mutated alleles might be expected as that this case represents a patient that had not received anti-EGFR therapy so no selection pressure for increased expression of the resistance mutation was present.

Another lung FFPE sample was assayed for a G719A EGFR mutation in combination with a S127F mutation of the tumor suppressor gene TP53. The in situ analysis of this tissue showed cells in stromal regions that only expressed the wild-type form of TP53 while no expression of any of the EGFR alleles could be detected. Hematoxylin and eosin (HE) staining of this tissue sample confirmed that the cell populations with wild-type TP53 were lymphocytes. The TP53 S127F mutation-positive tumor regions displayed signals from both the wild-type EGFR and G719A padlock probes but none from wild-type TP53 padlock probe, indicating TP53 LOH.

A set of padlock probes was applied on a FFPE lung tissue sample with reported KRAS G12C and TP53 P190S mutations. In contrast to the previous case, in which the wild-type and mutant TP53 signals were located in different compartments (stroma and tumor respectively), here the mutant and wild-type TP53 transcripts were expressed in a heterozygous fashion in the tumor compartment. Similarly the wild-type and mutant KRAS signals were evenly distributed across the tumor areas with a higher expression of mutant compared to wild-type KRAS alleles. This difference in expression pattern of the wild-type and mutant alleles in the two cases would not have been identified unless an in situ technique was included as a complement to DNA sequencing. Moreover, since this in situ assay reveals information on a single cell level, unique information (e.g. expression of more than one mutation in the same cell, can be identified and studied in detail. Co-localization of different alleles in the same cell provides strong evidence of their co-existence in cells in the tumor while absence of co-localization does not prove that they are not co-expressed in a certain cell-lineage. Even though all four alleles were not detected in any of these cells, the most likely interpretation of the staining pattern in is that the KRAS mutation is carried by all TP53 mutation-positive cells.

Discussion of Examples 11 to 17

Examples 11 to 17 document the establishment of a multiplex in situ assay that specifically targets point mutations on tumor tissue sections and on cytological preparations. Transcripts, synthesized by reverse transcription of mRNA in situ, are targeted with mutant- or wild-type specific padlock probes and amplified to a detectable level with RCA. The resulting wild-type and mutated products are thereafter labeled with fluorophores of different colors. This padlock probe-based assay demonstrates for the first time that mutation analysis for molecular cancer diagnostics can be performed directly on tumor tissue sections. A multiplexed in situ assay was developed and validated as a proof-of-concept for the activating point mutations in KRAS codon 12 and 13 that are associated with resistance to anti-EGFR therapy in colorectal cancer. The selectivity of the probes was first tested individually. There was a clear-cut distinction between the KRAS mutant and wild-type samples and the genotypes were easily determined by simple microscopic visualization of the corresponding fluorescent signals. For multiplex detection, a side-by-side comparison between single corresponding padlock pairs and a cocktail of all codon 12 and 13 KRAS padlock probes showed that the two approaches were similar in efficiency and specificity. The padlock strategy was developed on unfixed tissue preparations as fresh frozen tissue contains high quality DNA and RNA and serves as the golden standard for molecular studies. However, implementation of diagnostics on fresh frozen tissue requires substantial and expensive biobanking efforts. As an alternative, unfixed tumor cells were used on touch imprints from the fresh cut tumor surface. The KRAS mutation status could thus be determined on the day of sample arrival and was concordant with our routine pyrosequencing assay.

FFPE tissue blocks are used globally in routine surgical pathology and can be preserved for years in tissue archives. However, crosslinking of biomolecules induced by formalin results in fragmentation of DNA and RNA. Nevertheless, the short length of the padlock probe, in combination with the requirement of dual recognition sites and ligation makes this assay ideal for fixed histopathology specimens. Using a protocol optimized for formalin-fixed tissues in situ detection in routine FFPE sections was achieved and prospective surgical cancer specimens with unknown KRAS status were successfully characterized. A promising prospect for this assay is that hundreds of FFPE cancer samples can be screened simultaneously in TMAs for presence of mutations. Thus, for biomarker discovery in retrospective patient cohorts with available TMAs, high-throughput screening for point mutations could be performed along with IHC for protein expression and FISH-analysis for chromosomal aberration. The in situ protocol can be adapted for automation as any conventional FISH-assay, facilitating implementation of the assay for routine use. Moreover, the fluorescence readout can be changed to a histochemical staining for brightfield imaging if desired.

Tumor heterogeneity is a complex concept. One aspect is the variable mixture of cancer cells with acquired somatic mutations and genetically normal stromal and inflammatory cells. A second aspect is the morphological, and possibly genetic, variation within the tumor compartment with regard to pre-neoplastic versus invasive components, high-grade versus low-grade areas, invasion front versus central tumor area, and variable differentiation patterns, e.g. sarcomatoid, glandular, squamous or neuroendocrine etc. A third aspect is that the expression of a mutated allele can be influenced by promoter and splicing mutations, epigenetic alteration, or gene copy number aberrations, e.g. amplifications, deletions and LOH, in different parts of the tumor. These may be challenging to analyze on a genomic level. The described in situ technique allows studies of all these challenging features of tumor heterogeneity. Heterozygous and homozygous expression of mutated and wild-type alleles can be appreciated in tumor cells and demonstrate one form of fundamental information about a particular tissue specimen that probably would have gone undetected with PCR-based techniques resulting in an average value of the extracted mixture of mutant tumor and wild-type cells. This assay shows increased expression of a mutated KRAS codon 61 allele along with tumor progression in a colon cancer sample. In a case of lung adenocarcinoma, the expression of an activating EGFR mutation was demonstrated to be different in areas with distinctive histological architecture. Moreover, the technique allows dissection of how multiple different mutations are distributed and associated across a tumor lesion, as illustrated by two lung cancer cases where mutated TP53 alleles could be visualized together with activating mutations in EGFR and KRAS respectively. Thus, mutation analysis in situ can help to dissect processes such as cancer initiation, tumor progression and metastasis. For future studies an intriguing application will be studies of the emergence of resistance mutations in response to targeted therapy. One case with a double mutation in EGFR was presented where low expression of the resistance mutation was seen in parallel with expression of the mutation associated with treatment response, as might be expected in a patient with a de novo resistance mutation. Analysis of a follow-up sample after EGFR treatment could reveal a patient-specific response on a histological level regarding the expression of the two mutations.

Despite the fact that the 79 patient samples assayed in this study had been collected at different time points during the last two decades, as well as treated under various conditions, they all qualified as suitable tissue material for this presented method. Furthermore, specifically designed padlock probes were successfully applied for in situ detection of totally 14 different point mutations which give confidence that this mutation assay offers robustness and can easily be adapted for detection of other mutations on tissue material from various sources. In conclusion, the presented padlock probe and RCA technology is believed to be an important assay for studies of histologic-genotypic correlations in complex tumor tissues for diagnostic molecular pathology and translational cancer research.

Example 18 Detection of Braf Mutations

BRAF presents somatic mutations in different sort of tumors, predominantly in malignant melanoma, sporadic colorectal tumors showing mismatch repair defects in microsatellites (MSI), low-grade ovarian serous carcinoma and thyroid papillary cancer. 80% of these mutations correspond to the hotspot transversion mutation T1799A that causes the amino acidic substitution V600E.

Most common mutation is the V600E mutation (Substitution—Missense) Target cDNA region (mutated base):

(SEQ ID NO: 100) 5′GCATATACATCTGACTGAAAGCTGTATGGATTTTTATCTTGCATTCT GATGACTTCTGGTGCCATCCACAAAATGGATCCAGACAACTGTTCAAAC TGATGGGACCCACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCAC CTA-3′ BRAF padlock probe target region (arms: 15+15 nt):

(SEQ ID NO: 101) 5′-CTCCATCGAGATTTCACTGTAGCTAGACCA-3′

REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

-   Botling and Micke, Methods Mol. Biol., 675:299-306, 2011. -   Lagunavicius et al., RNA, 15:765-771, 2009. -   Larsson et al., Nat. Methods, 1:227-232, 2004. -   Lizardi et al., Nat. Genet., 19:225-232, 1998. -   Mitra and Church, Nucleic Acids Res., 27(24), 1999. -   Nilsson et al., Nat. Biotechnol., 18:791-793, 2000. -   Nilsson et al., Nucleic Acid Res., 29:578-581, 2001. -   Nilsson et al., Science, 265:2085-2088, 1994. -   Owczarzy et al., Biochemistry, 47:5336-5353, 2008. -   PCT Appln. WO 99/49079 -   Pena et al., Nat. Methods, 6(2):139-141, 2009. -   Sambrook et al., Molecular Cloning—A Laboratory Manual, Cold Spring     Harbor Laboratory, NY, 1989. -   Stougaard et al., BMC Biotech., 7:69, 2007. -   Sundstrom et al., BMC Cancer, 10:660, 2010. -   Wetmur, Critical Rev. Biochem. Mol. Biol., 26(3/4):227-259, 1991. -   Yi et al., Nucleic Acid Res., 29:4818-4825, 2001. 

What is claimed:
 1. A method for evaluating a nucleic acid sequence in a tissue section comprising: incubating an RNA containing the nucleic acid sequence in the tissue section with a reverse transcriptase and a reverse transcription primer that is complementary to the RNA to generate cDNA, wherein the reverse transcription primer is modified so as to be capable of immobilization in the cells of the tissue section; digesting all or part of the RNA; hybridizing one or more padlock probes to the cDNA, wherein the padlock probe(s) comprise one or two terminal regions having the nucleic acid sequence; incubating the hybridized padlock probe(s) and cDNA with ligase under conditions to ligate the ends of the padlock probe(s); incubating the padlock probe(s) with a polymerase to create an amplified rolling circle amplification product; and, sequencing the amplified rolling circle amplification product.
 2. The method of claim 1, wherein the sample is on a solid support.
 3. The method of claim 2, wherein the solid support is a slide.
 4. The method of claim 3, wherein the slide has a cover.
 5. The method of claim 2, wherein the tissue sample is removed from the solid support prior to sequencing.
 6. The method of claim 1, wherein the cells are stained.
 7. The method of claim 6, wherein the cells are stained with hematoxylin and eosin.
 8. The method of claim 1, wherein the reverse transcription primer has a functional moiety capable of binding to or reacting with a cell or cellular component or an affinity binding group capable of binding to a cell or cellular component.
 9. The method of claim 1, wherein the reverse transcription primer comprises at least one nucleotide modified with biotin, an amine group, a lower alkylamine group, an acetyl group, DMTO, fluoroscein, a thiol group, or acridine.
 10. The method of claim 9, wherein the reverse transcription primer comprises one or more locked nucleic acid residues.
 11. The method of claim 10, wherein the reverse transcription primer comprises 2 or more locked nucleic acids separated by 1 or more natural or synthetic nucleotides in the primer sequence.
 12. The method of claim 1, further comprising adding a ribonuclease to digest RNA hybridized to the cDNA.
 13. The method of claim 1, wherein the rolling circle amplification uses a DNA polymerase having 3′-5′ exonuclease activity wherein if necessary the exonuclease activity digests the cDNA to generate a free 3′ end which acts as a primer for the RCA.
 14. The method of claim 13, wherein the DNA polymerase is a Φ29 polymerase.
 15. The method of claim 1, further comprising contacting the sample with an exonuclease to digest the cDNA to generate a free 3′ end which acts as a primer for the RCA.
 16. The method of claim 1, wherein sequencing involves one or more chain terminating nucleotides.
 17. The method of claim 1, wherein sequencing comprises mass spectroscopy.
 18. The method of claim 1, wherein in the contacting step, the sample is contacted with at least a first and a second padlock probe, wherein the first padlock probe comprises terminal regions complementary to immediately adjacent regions on the cDNA, and wherein the second padlock probe comprises terminal regions that differ from the terminal regions of the first padlock probe only by a single nucleotide at the 5′ or 3′ terminus of the second padlock probe.
 19. The method of claim 1, wherein multiple different RNAs are detected using multiple different padlock probes.
 20. The method of claim 1, wherein subjecting the circularized padlock probe(s) to rolling circle amplification comprises adding labeled nucleotides to generate labeled, amplified padlock(s).
 21. The method claim of 1, wherein RNA is detected in a single cell.
 22. The method of claim 1, wherein the sample comprises a fixed tissue section, touch imprint samples, a formalin-fixed paraffin-embedded tissue section or a cytological preparation comprising one or more cells.
 23. The method of claim 22, wherein the tissue section is a formalin-fixed paraffin-embedded tissue section.
 24. The method of claim 1, wherein the tissue section is a colon, lung, pancreas, prostate, skin, thyroid, liver, ovary, endometrium, kidney, brain, testis, lymphatic fluid, blood, plasma, urinary bladder, or breast sample.
 25. A method for determining in situ a nucleic acid sequence in a formalin-fixed paraffin-embedded tissue section comprising: generating a cDNA complementary to an RNA containing the nucleic acid sequence in the tissue section; incubating the cDNA with a ribonuclease in the sample to digest the RNA; hybridizing one or more padlock probes to the cDNA, wherein the padlock probe(s) comprise one or two terminal regions having the nucleic acid sequence; incubating the hybridized padlock probes and cDNA with ligase under conditions to ligate the ends of the padlock probe(s); replicating the padlock probe(s) using a polymerase to create an amplified product; sequencing the complement of the nucleic acid sequence in the amplified product to determine the nucleic acid sequence and/or its complement.
 26. The method of claim 25, wherein the sequencing comprises performing mass spectroscopy. 